Peptides and combination of peptides for use in immunotherapy against prostate cancer and other cancers

ABSTRACT

A method of treating a patient who has prostate cancer includes administering to said patient a composition containing a population of activated T cells that selectively recognize cells in the patient that aberrantly express a peptide. A pharmaceutical composition contains activated T cells that selectively recognize cells in a patient that aberrantly express a peptide, and a pharmaceutically acceptable carrier, in which the T cells bind to the peptide in a complex with an MHC class I molecule, and the composition is for treating the patient who has prostate cancer. A method of treating a patient who has prostate cancer includes administering to said patient a composition comprising a peptide in the form of a pharmaceutically acceptable salt, thereby inducing a T-cell response to the prostate cancer.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is continuation of U.S. application Ser. No. 15/229,970filed 5 Aug. 2016, which claims priority from UK Patent Application No1513921.5 filed 6 Aug. 2015 and U.S. Provisional Application No.62/201,289 filed 5 Aug. 2015 both of which are incorporated herein byreference in their entireties.

This application is also related to PCT/EP2016/068727 filed 5 Aug. 2016,the content of which is incorporated herein by reference in itsentirety.

REFERENCE TO SEQUENCE LISTING SUBMITTED AS A COMPLIANT ASCII TEXT FILE(.TXT)

Pursuant to the EFS-Web legal framework and 37 CFR §§ 1.821-825 (seeMPEP § 2442.03(a)), a Sequence Listing in the form of an ASCII-complianttext file (entitled “2912919-053003_ST25.txt” created on 22 Jun. 2016,and 9,608 bytes in size) is submitted concurrently with the instantapplication, and the entire contents of the Sequence Listing areincorporated herein by reference.

FIELD OF THE INVENTION

The present invention relates to peptides, proteins, nucleic acids andcells for use in immunotherapeutic methods. In particular, the presentinvention relates to the immunotherapy of cancer. The present inventionfurthermore relates to tumor-associated T-cell peptide epitopes, aloneor in combination with other tumor-associated peptides that can forexample serve as active pharmaceutical ingredients of vaccinecompositions that stimulate anti-tumor immune responses, or to stimulateT cells ex vivo and transfer into patients. Peptides bound to moleculesof the major histocompatibility complex (MHC), or peptides as such, canalso be targets of antibodies, soluble T-cell receptors, and otherbinding molecules.

The present invention relates to several novel peptide sequences andtheir variants derived from HLA class I molecules of human tumor cellsthat can be used in vaccine compositions for eliciting anti-tumor immuneresponses, or as targets for the development ofpharmaceutically/immunologically active compounds and cells.

BACKGROUND OF THE INVENTION

Prostate cancer is the second most frequently diagnosed cancer worldwideand the fifth most common cause of cancer death among men, with anestimated 1.1 million new cases (15% of all cancers in men) and 0.3million cancer deaths (7% of all cancer deaths in men) in 2012. In thesame period it was the most frequent type of cancer among men 84countries worldwide, largely in countries that have attained high orvery high levels of human development, but also in several countries inCentral and Southern Africa. An estimated 220,800 new cases of prostatecancer and 27,540 deaths due to prostate cancer are expected in 2015 inthe USA according to the American Cancer Society. Risk factors forprostate cancer are age, family history, and race (World Cancer Report,2014; SEER Stat facts, 2014; American Cancer Society, 2015).

Almost all prostate cancers are adenocarcinomas which develop from thegland cells of the prostate. Rare forms of prostate cancer includesarcomas, small cell carcinomas, neuroendocrine tumors (other than smallcell carcinomas) or transitional cell carcinomas (American CancerSociety, 2015).

The therapeutic strategy for prostate cancer mainly depends on thecancer stage. For locally restricted non-metastasizing prostate cancer,treatment options include active surveillance (wait and watch), completesurgical resection of the prostate and local high dose radiation therapywith or without brachytherapy. In high risk patients, hormonal ablationtherapy and post-operative local radiation therapy represent furtherpossibilities. Standard treatments for metastasizing prostate canceralso comprise complete surgical resection of the prostate, local highdose radiation and hormonal ablation therapy. Tumors irresponsive tohormonal deprivation are called castration-resistant prostate cancers(CRPC). CRPC patients receive docetaxel, abiraterone and the dendriticcell-based vaccine sipuleucel-T. Bone metastases are treated withradium-223 alone or a combination of either radium-223, docetaxel orabiraterone with bisphosphonates or denosumab (S3-LeitlinieProstatakarzinom, 2014).

The dendritic cell-based vaccine sipuleucel-T was the first anti-cancervaccine to be approved by the FDA. Due to its positive effect onsurvival in patients with CRPC, much effort is put into the developmentof further immunotherapies. Regarding vaccination strategies, thepeptide vaccine prostate-specific antigen (PSA)-TRICOM, the personalizedpeptide vaccine PPV, the DNA vaccine pTVG-HP and the whole cell vaccineexpressing GM-CSF GVAX showed promising results in different clinicaltrials. Furthermore, dendritic cell-based vaccines other thansipuleucel-T, namely BPX-101 and DCVAC/Pa were shown to elicitedclinical responses in prostate cancer patients. Immune checkpointinhibitors like ipilimumab and nivolumab are currently evaluated inclinical studies as monotherapy as well as in combination with othertreatments, including androgen deprivation therapy, local radiationtherapy, PSA-TRICOM and GVAX. The immunomodulatory substancetasquinimod, which significantly slowed progression and increasedprogression free survival in a phase II trial, is currently furtherinvestigated in a phase III trial. Lenalidomide, anotherimmunomodulator, induced promising effects in early phase clinicalstudies, but failed to improve survival in a phase III trial. Despitethese disappointing results further lenalidomide trials are ongoing(Quinn et al., 2015).

Considering the severe side-effects and expense associated with treatingcancer, there is a need to identify factors that can be used in thetreatment of cancer in general and prostate cancer in particular. Thereis also a need to identify factors representing biomarkers for cancer ingeneral and prostate cancer in particular, leading to better diagnosisof cancer, assessment of prognosis, and prediction of treatment success.

Immunotherapy of cancer represents an option of specific targeting ofcancer cells while minimizing side effects. Cancer immunotherapy makesuse of the existence of tumor associated antigens.

The current classification of tumor associated antigens (TAAs) comprisesthe following major groups:

-   a) Cancer-testis antigens: The first TAAs ever identified that can    be recognized by T cells belong to this class, which was originally    called cancer-testis (CT) antigens because of the expression of its    members in histologically different human tumors and, among normal    tissues, only in spermatocytes/spermatogonia of testis and,    occasionally, in placenta. Since the cells of testis do not express    class I and II HLA molecules, these antigens cannot be recognized by    T cells in normal tissues and can therefore be considered as    immunologically tumor-specific. Well-known examples for CT antigens    are the MAGE family members and NY-ESO-1.-   b) Differentiation antigens: These TAAs are shared between tumors    and the normal tissue from which the tumor arose. Most of the known    differentiation antigens are found in melanomas and normal    melanocytes. Many of these melanocyte lineage-related proteins are    involved in biosynthesis of melanin and are therefore not tumor    specific but nevertheless are widely used for cancer immunotherapy.    Examples include, but are not limited to, tyrosinase and    Melan-A/MART-1 for melanoma or PSA for prostate cancer.-   c) Over-expressed TAAs: Genes encoding widely expressed TAAs have    been detected in histologically different types of tumors as well as    in many normal tissues, generally with lower expression levels. It    is possible that many of the epitopes processed and potentially    presented by normal tissues are below the threshold level for T-cell    recognition, while their over-expression in tumor cells can trigger    an anticancer response by breaking previously established tolerance.    Prominent examples for this class of TAAs are Her-2/neu, survivin,    telomerase, or WT1.-   d) Tumor-specific antigens: These unique TAAs arise from mutations    of normal genes (such as β-catenin, CDK4, etc.). Some of these    molecular changes are associated with neoplastic transformation    and/or progression. Tumor-specific antigens are generally able to    induce strong immune responses without bearing the risk for    autoimmune reactions against normal tissues. On the other hand,    these TAAs are in most cases only relevant to the exact tumor on    which they were identified and are usually not shared between many    individual tumors. Tumor-specificity (or -association) of a peptide    may also arise if the peptide originates from a tumor-(-associated)    exon in case of proteins with tumor-specific (-associated) isoforms.-   e) TAAs arising from abnormal post-translational modifications: Such    TAAs may arise from proteins which are neither specific nor    overexpressed in tumors but nevertheless become tumor associated by    posttranslational processes primarily active in tumors. Examples for    this class arise from altered glycosylation patterns leading to    novel epitopes in tumors as for MUC1 or events like protein splicing    during degradation which may or may not be tumor specific.-   f) Oncoviral proteins: These TAAs are viral proteins that may play a    critical role in the oncogenic process and, because they are foreign    (not of human origin), they can evoke a T-cell response. Examples of    such proteins are the human papilloma type 16 virus proteins, E6 and    E7, which are expressed in cervical carcinoma.

T-cell based immunotherapy targets peptide epitopes derived fromtumor-associated or tumor-specific proteins, which are presented bymolecules of the major histocompatibility complex (MHC). The antigensthat are recognized by the tumor specific T lymphocytes, that is, theepitopes thereof, can be molecules derived from all protein classes,such as enzymes, receptors, transcription factors, etc. which areexpressed and, as compared to unaltered cells of the same origin,usually up-regulated in cells of the respective tumor.

Like for all cancer entities evolving from non-vital organs or tissues,prostate-specific antigens may be a good choice for cancer immunotherapybecause prostate-specific antigens represent tumor-specific targets in aprostatectomized patient. In a cancer patient without prostatectomy,such antigens may also be interesting because prostate is not regardedas a vital organ, and a similar approach has been taken in melanoma withmelanocyte differentiation antigens. There are several examples showingthat prostate-specific or highly-prostate-associated antigens are safetargets, e.g. sipuleucel-T (Provenge) from Dendreon comprising prostateacid phosphatase as used tumor antigen (Westdorp et al., 2014). Thisantigen is not exclusively expressed in prostate but over-expressed atlevels of 1-2 orders of magnitude higher in prostate vs. other tissues(Graddis et al., 2011).

There are two classes of MHC-molecules, MHC class I and MHC class II.MHC class I molecules are composed of an alpha heavy chain andbeta-2-microglobulin, MHC class II molecules of an alpha and a betachain. Their three-dimensional conformation results in a binding groove,which is used for non-covalent interaction with peptides.

MHC class I molecules can be found on most nucleated cells. They presentpeptides that result from proteolytic cleavage of predominantlyendogenous proteins, defective ribosomal products (DRIPs) and largerpeptides. However, peptides derived from endosomal compartments orexogenous sources are also frequently found on MHC class I molecules.This non-classical way of class I presentation is referred to ascross-presentation in the literature (Brossart and Bevan, 1997; Rock etal., 1990). MHC class II molecules can be found predominantly onprofessional antigen presenting cells (APCs), and primarily presentpeptides of exogenous or transmembrane proteins that are taken up byAPCs e.g. during endocytosis, and are subsequently processed.

Complexes of peptide and MHC class I are recognized by CD8-positive Tcells bearing the appropriate T-cell receptor (TCR), whereas complexesof peptide and MHC class II molecules are recognized byCD4-positive-helper-T cells bearing the appropriate TCR. It is wellknown that the TCR, the peptide and the MHC are thereby present in astoichiometric amount of 1:1:1.

CD4-positive helper T cells play an important role in inducing andsustaining effective responses by CD8-positive cytotoxic T cells. Theidentification of CD4-positive T-cell epitopes derived from tumorassociated antigens (TAA) is of great importance for the development ofpharmaceutical products for triggering anti-tumor immune responses(Gnjatic et al., 2003). At the tumor site, T helper cells, support acytotoxic T cell-(CTL) friendly cytokine milieu (Mortara et al., 2006)and attract effector cells, e.g. CTLs, natural killer (NK) cells,macrophages, and granulocytes (Hwang et al., 2007).

In the absence of inflammation, expression of MHC class II molecules ismainly restricted to cells of the immune system, especially professionalantigen-presenting cells (APC), e.g., monocytes, monocyte-derived cells,macrophages, dendritic cells. In cancer patients, cells of the tumorhave been found to express MHC class II molecules (Dengjel et al.,2006).

Elongated (longer) peptides of the invention can act as MHC class IIactive epitopes. T-helper cells, activated by MHC class II epitopes,play an important role in orchestrating the effector function of CTLs inanti-tumor immunity. T-helper cell epitopes that trigger a T-helper cellresponse of the TH1 type support effector functions of CD8-positivekiller T cells, which include cytotoxic functions directed against tumorcells displaying tumor-associated peptide/MHC complexes on their cellsurfaces. In this way tumor-associated T-helper cell peptide epitopes,alone or in combination with other tumor-associated peptides, can serveas active pharmaceutical ingredients of vaccine compositions thatstimulate anti-tumor immune responses.

It was shown in mammalian animal models, e.g., mice, that even in theabsence of CD8-positive T lymphocytes, CD4-positive T cells aresufficient for inhibiting manifestation of tumors via inhibition ofangiogenesis by secretion of interferon-gamma (IFNγ) (Beatty andPaterson, 2001; Mumberg et al., 1999). There is evidence for CD4 T cellsas direct anti-tumor effectors (Braumuller et al., 2013; Tran et al.,2014).

Since the constitutive expression of HLA class II molecules is usuallylimited to immune cells, the possibility of isolating class II peptidesdirectly from primary tumors was previously not considered possible.However, Dengjel et al. were successful in identifying a number of MHCClass II epitopes directly from tumors (WO 2007/028574, EP 1 760 088B1).

Since both types of response, CD8 and CD4 dependent, contribute jointlyand synergistically to the anti-tumor effect, the identification andcharacterization of tumor-associated antigens recognized by either CD8+T cells (ligand: MHC class I molecule+peptide epitope) or byCD4-positive T-helper cells (ligand: MHC class II molecule+peptideepitope) is important in the development of tumor vaccines.

For an MHC class I peptide to trigger (elicit) a cellular immuneresponse, it also must bind to an MHC-molecule. This process isdependent on the allele of the MHC-molecule and specific polymorphismsof the amino acid sequence of the peptide. MHC-class-I-binding peptidesare usually 8-12 amino acid residues in length and usually contain twoconserved residues (“anchors”) in their sequence that interact with thecorresponding binding groove of the MHC-molecule. In this way each MHCallele has a “binding motif” determining which peptides can bindspecifically to the binding groove.

In the MHC class I dependent immune reaction, peptides not only have tobe able to bind to certain MHC class I molecules expressed by tumorcells, they subsequently also have to be recognized by T cells bearingspecific T cell receptors (TCR).

For proteins to be recognized by T-lymphocytes as tumor-specific or-associated antigens, and to be used in a therapy, particularprerequisites must be fulfilled. The antigen should be expressed mainlyby tumor cells and not, or in comparably small amounts, by normalhealthy tissues. In a preferred embodiment, the peptide should beover-presented by tumor cells as compared to normal healthy tissues. Itis furthermore desirable that the respective antigen is not only presentin a type of tumor, but also in high concentrations (i.e. copy numbersof the respective peptide per cell). Tumor-specific and tumor-associatedantigens are often derived from proteins directly involved intransformation of a normal cell to a tumor cell due to their function,e.g. in cell cycle control or suppression of apoptosis. Additionally,downstream targets of the proteins directly causative for atransformation may be up-regulated and thus may be indirectlytumor-associated. Such indirect tumor-associated antigens may also betargets of a vaccination approach (Singh-Jasuja et al., 2004). It isessential that epitopes are present in the amino acid sequence of theantigen, in order to ensure that such a peptide (“immunogenic peptide”),being derived from a tumor associated antigen, leads to an in vitro orin vivo T-cell-response.

Basically, any peptide able to bind an MHC molecule may function as aT-cell epitope. A prerequisite for the induction of an in vitro or invivo T-cell-response is the presence of a T cell having a correspondingTCR and the absence of immunological tolerance for this particularepitope.

Therefore, TAAs are a starting point for the development of a T cellbased therapy including but not limited to tumor vaccines. The methodsfor identifying and characterizing the TAAs are usually based on the useof T-cells that can be isolated from patients or healthy subjects, orthey are based on the generation of differential transcription profilesor differential peptide expression patterns between tumors and normaltissues. However, the identification of genes over-expressed in tumortissues or human tumor cell lines, or selectively expressed in suchtissues or cell lines, does not provide precise information as to theuse of the antigens being transcribed from these genes in an immunetherapy. This is because only an individual subpopulation of epitopes ofthese antigens are suitable for such an application since a T cell witha corresponding TCR has to be present and the immunological tolerancefor this particular epitope needs to be absent or minimal. In a verypreferred embodiment of the invention it is therefore important toselect only those over- or selectively presented peptides against whicha functional and/or a proliferating T cell can be found. Such afunctional T cell is defined as a T cell, which upon stimulation with aspecific antigen can be clonally expanded and is able to executeeffector functions (“effector T cell”).

In case of targeting peptide-MHC by specific TCRs (e.g. soluble TCRs)and antibodies or other binding molecules (scaffolds) according to theinvention, the immunogenicity of the underlying peptides is secondary.In these cases, the presentation is the determining factor.

SUMMARY OF THE INVENTION

In a first aspect of the present invention, the present inventionrelates to a peptide comprising an amino acid sequence selected from thegroup consisting of SEQ ID No: 1 to SEQ ID No: 48 or a variant sequencethereof which is at least 77%, preferably at least 88%, homologous(preferably at least 77% or at least 88% identical) to SEQ ID No: 1 toSEQ ID No: 48, wherein said variant binds to MHC and/or induces T cellscross-reacting with said peptide, or a pharmaceutical acceptable saltthereof, wherein said peptide is not the underlying full-lengthpolypeptide.

The present invention further relates to a peptide of the presentinvention comprising a sequence that is selected from the groupconsisting of SEQ ID No: 1 to SEQ ID No: 48 or a variant thereof, whichis at least 77%, preferably at least 88%, homologous (preferably atleast 77% or at least 88% identical) to SEQ ID No: 1 to SEQ ID No: 48,wherein said peptide or variant thereof has an overall length of between8 and 100, preferably between 8 and 30, and most preferred of between 8and 14 amino acids.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1S depict embodiments as described herein.

FIGS. 2A-2E depict embodiments as described herein.

FIGS. 3A, 3B, 4A, 4B, 4C, 5A and 5B depict embodiments as describedherein.

DETAILED DESCRIPTION OF A PREFERRED EMBODIMENT

The following tables show the peptides according to the presentinvention, their respective SEQ ID Nos, and the prospective source(underlying) genes for these peptides. All peptides in Table 1, Table 3and Table 5 bind to HLA-A*02. All peptides in Table 2, Table 4 and Table6 bind to HLA-A*24. The peptides in Table 3 and Table 4 have beendisclosed before in large listings as results of high-throughputscreenings with high error rates or calculated using algorithms, buthave not been associated with cancer at all before. The peptides inTable 5 and Table 6 are additional peptides that may be useful incombination with the other peptides of the invention. The peptides inTable 7 and Table 8 are furthermore useful in the diagnosis and/ortreatment of various other malignancies that involve an over-expressionor over-presentation of the respective underlying polypeptide.

TABLE 1 HLA-A*02 peptides according to the present invention SEQ IDOfficial No. Sequence GeneID(s) Gene Symbol(s)  1 VTAQIGIVAV 81285OR51E2  2 SMLGEEIQL 9687 GREB1  3 HLLEDIAHV 4744 NEFH  4 ALLTFVWKL 79054TRPM8  5 KIFSRLIYI 79054 TRPM8  6 ALLESRVNL 50940 PDE11A  7  TLLQVVGVVSV10257 ABCC4  8 LLDFSLADA 1674 DES  9 GMLNEAEGKAIKL 4629 MYH11 10TLWRGPVVV 261729 STEAP2 11 YLEEECPAT 563 AZGP1 12 SLNEEIAFL 1674 DES 13AMAPNHAVV 4057 LTF 14 KMDEASAQLL 54682 MANSC1 15 KMDEASAQLLA 54682MANSC1 16 KMDEASAQL 54682 MANSC1 17 RLGIKPESV 1466 CSRP2 18 GLSEFTEYL4131 MAP1B 19 LLPPPPLLA 23245 ASTN2 20 SLLSHQVLL 57221 KIAA1244 21YLNDSLRHV 283078 MKX 22 SLYDSIAFI 56978 PRDM8 23 AVAGADVIITV 1428 CRYM

TABLE 2 HLA-A*24 peptides according to the present invention. SEQ IDOfficial No. Sequence GeneID(s) Gene Symbol(s) 24 SYNDALLTF 79054 TRPM825 IYEPYLAMF 79054 TRPM8 26 RYADDTFTPAF 5865 RAB3B 27 GYLQGLVSF 9622KLK4 28 YYAKEIHKF 7043 TGFB3 29 RYGSPINTF 647024 C6orf132 30 SYSPAHARL2624 GATA2 31 AYTSPPSFF 171024 SYNP02 32 PYQLNASLFTF 171024 SYNP02 33QYGKDFLTL 79088 ZNF426 34 AFSPDSHYLLF 3679 ITGA7 35 IYTRVTYYL64499, 7177 TPSB2, TPSAB1 36 RYMWINQEL 374654 KIF7 37 RYLQDLLAW 5339PLEC 38 VYSDKLWIF 8216 LZTR1 39 SYIDVAVKL 57544 TXNDC16

TABLE 3 Additional HLA-A*02 peptides according to thepresent invention with no known cancer association. J =phospho-serine prior SEQ ID Official  No. Sequence GeneID(s)Gene Symbol(s) 40 RTFJPTYGL 23336 SYNM

TABLE 4 Additional HLA-A*24 peptides according to thepresent invention with no prior known cancer association SEQ IDOfficial  No. Sequence GeneID(s) Gene Symbol(s) 41 RYLQKIEEF 3755 KCNG142 TYIGQGYII 60681 FKBP10 43 AYIKNGQLF 56978 PRDM8 44 VYNTVSEGTHF 258005L039A6 45 RYFKTPRKF 25792 CIZ1 46 VYEEILHQI 116496 FAM129A 47 SYTPVLNQF10497 UNC13B 48 AWAPKPYHKF 23043, 50488, TNIK, MINK1,  9448 MAP4K4

TABLE 5 HLA-A*02 peptides useful for e.g. personalized cancer therapiesSEQ ID Official  No. Sequence GeneID(s) Gene Symbol(s) 49 SLFHPEDTGQV354 KLK3 50 TLGPASFLV 389816 LRRC26 51 AMFDKKVQL 23336 SYNM 52 ALGDLVQSV7782 SLC30A4 53 YLLKDKGEYTL 2316 FLNA

TABLE 6 HLA-A*24 peptides useful for e.g. personalized cancer therapiesSEQ ID Official  No. Sequence GeneID(s) Gene Symbol(s) 54 AYSEKVTEF 3817KLK2 55 LYFEKGEYF 55 ACPP 56 LFHPEDTGQVF 354 KLK3 57 KYADKIYSI 2346FOLH1 58 GYIDKVRQL 4744 NEFH 59 IYPDVTYAF 1135 CHRNA2

TABLE 7 Peptides according to the present invention and theirspecific uses in other proliferative diseases, especially in cancerous diseases. The table shows forselected peptides on which additional tumor types theywere found and either over-presented on more than 5% of the measured tumor samples, or presented on more than 5%of the measured tumor samples with a ratio of geometricmeans tumor vs normal tissues being larger than three. Over-presentation is defined as higher presentation on thetumor sample as compared to the normal sample with highestpresentation. Normal (non-cancerous) tissues against whichover-presentation was tested were selected from:adipose tissue, adrenal gland, artery, bone marrow, brain,central nerve, colon, duodenum, esophagus, eye,gallbladder, heart, kidney, liver, lung, lymph node,mononuclear white blood cells, pancreas, parathyroid gland,peripheral nerve, peritoneum, pituitary, pleura, rectum, salivary gland, skeletal muscle, skin, smallintestine, spleen, stomach, thyroid gland, trachea, ureter,urinary bladder, and veins. SEQ ID No. SequenceOther relevant organs/diseases  1 VTAQIGIVAV SCLC, Melanoma  2 SMLGEEIQLHCC, BRCA, Melanoma, Uterine Cancer  3 HLLEDIAHV MCC, Uterine Cancer  5KIFSRLIYI Melanoma  6 ALLESRVNL HCC, PC  7 TLLQVVGVVSVUterine Cancer, Gallbladder Cancer, Bile Duct Cancer  8 LLDFSLADACRC, BRCA, Melanoma, Urinary bladder cancer, Uterine Cancer 10 TLWRGPVVVNSCLC, RCC, CRC, HCC, Leukemia, OC, Esophageal Cancer, GallbladderCancer, Bile Duct Cancer, CLL 12 SLNEEIAFLSCLC, PC, Urinary bladder cancer, Gallbladder Cancer, Bile Duct Cancer13 AMAPNHAVV Brain Cancer 16 KMDEASAQL Urinary bladder cancer 17RLGIKPESV Brain Cancer, HCC, BRCA, Uterine Cancer 18 GLSEFTEYLBrain Cancer 19 LLPPPPLLA Brain Cancer, Melanoma, Urinary bladder cancer20 SLLSHQVLL SCLC, CRC, HCC, Urinary bladder cancer,BRCA, Esophageal Cancer, Uterine Cancer 22 SLYDSIAFIBrain Cancer, Leukemia, AML 26 RYADDTFTPAF HCC 27 GYLQGLVSF HCC 28YYAKEIHKF NSCLC, HCC 29 RYGSPINTF NSCLC, GC, HCC 31 AYTSPPSFF GC, HCC 33QYGKDFLTL NSCLC, Brain Cancer, HCC 34 AFSPDSHYLLFNSCLC, RCC, Brain Cancer, HCC 35 IYTRVTYYL NSCLC, GC 36 RYMWINQELNSCLC, Brain Cancer, HCC 37 RYLQDLLAW NSCLC, RCC, Brain Cancer 38VYSDKLWIF NSCLC, Brain Cancer, GC, HCC 40 RTFJPTYGLUrinary bladder cancer 41 RYLQKIEEF NSCLC, RCC, Brain Cancer 42TYIGQGYII NSCLC, Brain Cancer, GC, HCC 43 AYIKNGQLF Brain Cancer 44VYNTVSEGTHF NSCLC, Brain Cancer, HCC 45 RYFKTPRKF HCC 47 SYTPVLNQF HCC48 AWAPKPYHKF NSCLC, RCC, Brain Cancer, HCC NSCLC = non-small cell lungcancer, SCLC = small cell lung cancer, RCC = kidney cancer, CRC = colonor rectum cancer, HCC = liver cancer, PC = pancreatic cancer, BRCA =breast cancer, MCC = Merkel cell carcinoma, OC = ovarian cancer, AML =acute myeloid leukemia, CLL= chronic lymphocytic leukemia, GC = stomachcancer; J = phophoserine

The present invention furthermore generally relates to the peptidesaccording to the present invention for use in the treatment ofproliferative diseases, such as, for example, lung cancer, small celllung cancer, melanoma, liver cancer, breast cancer, Uterine cancer,Merkel cell carcinoma, pancreatic cancer, gallbladder cancer, bile ductcancer, CRC, urinary bladder cancer, non-small cell lung cancer, kidneycancer, Leukemia (e.g. AML or CLL), ovarian cancer, esophageal cancer,brain cancer, and gastric (stomach) cancer.

Particularly preferred are the peptides—alone or incombination—according to the present invention selected from the groupconsisting of SEQ ID No: 1 to SEQ ID No: 48. More preferred are thepeptides—alone or in combination—selected from the group consisting ofSEQ ID No: 1 to SEQ ID No: 6 (see Table 1) and SEQ ID No: 24 to SEQ IDNo: 28 (see Table 2) or SEQ ID No: 1, 4, 5, 6, 49, and 52 or SEQ ID No:2, 3, and 54, and their uses in the immunotherapy of lung cancer, smallcell lung cancer, melanoma, liver cancer, breast cancer, Uterine cancer,Merkel cell carcinoma, pancreatic cancer, gallbladder cancer, bile ductcancer, CRC, urinary bladder cancer, non-small cell lung cancer, kidneycancer, Leukemia (e.g. AML or CLL), ovarian cancer, esophageal cancer,brain cancer, and gastric (stomach) cancer, and most preferably prostatecancer. As shown in the above Table 7, many of the peptides according tothe present invention are also found on other tumor types and can, thus,also be used in the immunotherapy of other indications. Also refer toFIG. 1 and Example 1.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to anyone of SEQ ID No. 1, 12, and 20 for the—in one preferred embodimentcombined—treatment of non-small cell lung cancer.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to anyone of SEQ ID No. 1, 2, 5, 8, and 19 for the—in one preferred embodimentcombined—treatment of melanoma.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to anyone of SEQ ID No. 2, 6, 10, 17, 20, 26, 27, 28, 29, 31, 33, 34, 36, 38,42, 44, 45, 47, and 48 for the—in one preferred embodimentcombined—treatment of liver cancer.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to anyone of SEQ ID No. 2, 8, 17, and 20 for the—in one preferred embodimentcombined—treatment of breast cancer.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to anyone of SEQ ID No. 2, 3, 7, 8, 17, and 20 for the—in one preferredembodiment combined—treatment of uterine cancer.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to SEQ IDNo. 3 for the treatment of MCC.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to anyone of SEQ ID No. 6, and 12 for the—in one preferred embodimentcombined—treatment of PC.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to anyone of SEQ ID No. 7, 10, and 12 for the—in one preferred embodimentcombined—treatment of gallbladder cancer, and/or bile duct cancer.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to anyone of SEQ ID No. 8, 10, and 20 for the—in one preferred embodimentcombined—treatment of CRC.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to anyone of SEQ ID No. 10, and 22 for the—in one preferred embodimentcombined—treatment of leukemia.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to SEQ IDNo. 10 for the treatment of OC.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to anyone of SEQ ID No. 10, and 20 for the—in one preferred embodimentcombined—treatment of esophageal Cancer.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to SEQ IDNo. 10 for the treatment of CLL.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to anyone of SEQ ID No. 6, and 12 for the—in one preferred embodimentcombined—treatment of PC.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to anyone of SEQ ID No. 10, 28, 29, 33, 34, 35, 36, 37, 38, 41, 42, 44, and 48for the—in one preferred embodiment combined—treatment of NSCLC.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to anyone of SEQ ID No. 10, 34, 37, 41, and 48 for the—in one preferredembodiment combined—treatment of RCC.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to anyone of SEQ ID No. 13, 17, 18, 19, 22, 33, 34, 36, 37, 38, 41, 42, 43,44, and 48 for the—in one preferred embodiment combined—treatment ofbrain cancer.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to SEQ IDNo. 22 for the treatment of AML.

Thus, another aspect of the present invention relates to the use of atleast one peptide according to the present invention according to anyone of SEQ ID No. 29, 31, 35, 38, and 42 for the—in one preferredembodiment combined—treatment of GC.

Thus, another aspect of the present invention relates to the use of thepeptides according to the present invention for the—preferablycombined—treatment of a proliferative disease selected from the group oflung cancer, small cell lung cancer, melanoma, liver cancer, breastcancer, Uterine cancer, Merkel cell carcinoma, pancreatic cancer,gallbladder cancer, bile duct cancer, CRC, urinary bladder cancer,non-small cell lung cancer, kidney cancer, Leukemia (e.g. AML or CLL),ovarian cancer, esophageal cancer, brain cancer, and gastric (stomach)cancer, and most preferably prostate cancer.

The present invention furthermore relates to peptides according to thepresent invention that have the ability to bind to a molecule of thehuman major histocompatibility complex (MHC) class-I or—in an elongatedform, such as a length-variant—MHC class-II.

The present invention further relates to the peptides according to thepresent invention wherein said peptides (each) consist or consistessentially of an amino acid sequence according to SEQ ID No: 1 to SEQID No: 48.

The present invention further relates to the peptides according to thepresent invention, wherein said peptide is modified and/or includesnon-peptide bonds.

The present invention further relates to the peptides according to thepresent invention, wherein said peptide is part of a fusion protein, inparticular fused to the N-terminal amino acids of the HLA-DRantigen-associated invariant chain (Ii), or fused to (or into thesequence of) an antibody, such as, for example, an antibody that isspecific for dendritic cells.

Another embodiment of the present invention relates to a non-naturallyoccurring peptide wherein said peptide consists or consists essentiallyof an amino acid sequence according to SEQ ID No: 1 to SEQ ID No: 48 andhas been synthetically produced (e.g. synthesized) as a pharmaceuticallyacceptable salt. Methods to synthetically produce peptides are wellknown in the art. The salts of the peptides according to the presentinvention differ substantially from the peptides in their state(s) invivo, as the peptides as generated in vivo are no salts. The non-naturalsalt form of the peptide mediates the solubility of the peptide, inparticular in the context of pharmaceutical compositions comprising thepeptides, e.g. the peptide vaccines as disclosed herein. A sufficientand at least substantial solubility of the peptide(s) is required inorder to efficiently provide the peptides to the subject to be treated.Preferably, the salts are pharmaceutically acceptable salts of thepeptides. These salts according to the invention include alkaline andearth alkaline salts such as salts of the Hofmeister series comprisingas anions PO₄ ³⁻, SO₄ ²⁻, CH₃COO⁻, Cl⁻, Br⁻, NO₃ ⁻, ClO₄ ⁻, I⁻, SCN⁻ andas cations NH₄ ⁺, Rb⁺, K⁺, Na⁺, Cs⁺, Li⁺, Zn²⁺, Mg²⁺, Ca²⁺, Mn²⁺, Cu²⁺and Ba²⁺. Particularly salts are selected from (NH₄)₃PO₄, (NH₄)₂HPO₄,(NH₄)H₂PO₄, (NH₄)₂SO₄, NH₄CH₃COO, NH₄Cl, NH₄Br, NH₄NO₃, NH₄ClO₄, NH₄I,NH₄SCN, Rb₃PO₄, Rb₂HPO₄, RbH₂PO₄, Rb₂SO₄, Rb₄CH₃COO, Rb₄Cl, Rb₄Br,Rb₄NO₃, Rb₄ClO₄, R₄I, Rb₄SCN, K₃PO₄, K₂HPO₄, KH₂PO₄, K₂SO₄, KCH₃COO,KCl, KBr, KNO₃, KClO₄, KI, KSCN, Na₃PO₄, Na₂HPO₄, NaH₂PO₄, Na₂SO₄,NaCH₃COO, NaCl, NaBr, NaNO₃, NaClO₄, NaI, NaSCN, ZnCl₂ Cs₃PO₄, Cs₂HPO₄,CsH₂PO₄, Cs₂SO₄, CsCH₃COO, CsCl, CsBr, CsNO₃, CsClO₄, CsI, CsSCN,Li₃PO₄, Li₂HPO₄, LiH₂PO₄, Li₂SO₄, LiCH₃COO, LiCl, LiBr, LiNO₃, LiClO₄,LiI, LiSCN, Cu₂SO₄, Mg₃(PO₄)₂, Mg₂HPO₄, Mg(H₂PO₄)₂, Mg₂SO₄, Mg(CH₃COO)₂,MgCl₂, MgBr₂, Mg(NO₃)₂, Mg(ClO₄)₂, MgI₂, Mg(SCN)₂, MnCl₂, Ca₃(PO₄),Ca₂HPO₄, Ca(H₂PO₄)₂, CaSO₄, Ca(CH₃COO)₂, CaCl₂, CaBr₂, Ca(NO₃)₂,Ca(ClO₄)₂, CaI₂, Ca(SCN)₂, Ba₃(PO₄)₂, Ba₂HPO₄, Ba(H₂PO₄)₂, BaSO₄,Ba(CH₃COO)₂, BaCl₂, BaBr₂, Ba(NO₃)₂, Ba(ClO₄)₂, BaI₂, and Ba(SCN)₂.Particularly preferred are NH acetate, MgCl₂, KH₂PO₄, Na₂SO₄, KCl, NaCl,and CaCl₂, such as, for example, the chloride or acetate(trifluoroacetate) salts.

Generally, peptides and variants (at least those containing peptidelinkages between amino acid residues) may be synthesized by theFmoc-polyamide mode of solid-phase peptide synthesis as disclosed byLukas et al. (Lukas et al., 1981) and by references as cited therein.Temporary N-amino group protection is afforded by the9-fluorenylmethyloxycarbonyl (Fmoc) group. Repetitive cleavage of thishighly base-labile protecting group is done using 20% piperidine in N,N-dimethylformamide. Side-chain functionalities may be protected astheir butyl ethers (in the case of serine threonine and tyrosine), butylesters (in the case of glutamic acid and aspartic acid),butyloxycarbonyl derivative (in the case of lysine and histidine),trityl derivative (in the case of cysteine) and4-methoxy-2,3,6-trimethylbenzenesulphonyl derivative (in the case ofarginine). Where glutamine or asparagine are C-terminal residues, use ismade of the 4,4′-dimethoxybenzhydryl group for protection of the sidechain amido functionalities. The solid-phase support is based on apolydimethyl-acrylamide polymer constituted from the three monomersdimethylacrylamide (backbone-monomer), bisacryloylethylene diamine(cross linker) and acryloylsarcosine methyl ester (functionalizingagent). The peptide-to-resin cleavable linked agent used is theacid-labile 4-hydroxymethylphenoxyacetic acid derivative. All amino acidderivatives are added as their preformed symmetrical anhydridederivatives with the exception of asparagine and glutamine, which areadded using a reversed N,N-dicyclohexyl-carbodiimide/1hydroxybenzotriazole mediated couplingprocedure. All coupling and deprotection reactions are monitored usingninhydrine, trinitrobenzene sulphonic acid or isotin test procedures.Upon completion of synthesis, peptides are cleaved from the resinsupport with concomitant removal of side-chain protecting groups bytreatment with 95% trifluoroacetic acid containing a 50% scavenger mix.Scavengers commonly used include ethanedithiol, phenol, anisole andwater, the exact choice depending on the constituent amino acids of thepeptide being synthesized. Also a combination of solid phase andsolution phase methodologies for the synthesis of peptides is possible(see, for example, (Bruckdorfer et al., 2004), and the references ascited therein).

Trifluoroacetic acid is removed by evaporation in vacuo, with subsequenttrituration with diethyl ether affording the crude peptide. Anyscavengers present are removed by a simple extraction procedure which onlyophilization of the aqueous phase affords the crude peptide free ofscavengers. Reagents for peptide synthesis are generally available frome.g. Calbiochem-Novabiochem (Nottingham, UK).

Purification may be performed by any one, or a combination of,techniques such as recrystallization, size exclusion chromatography,ion-exchange chromatography, hydrophobic interaction chromatography and(usually) reverse-phase high performance liquid chromatography usinge.g. acetonitril/water gradient separation.

The present invention further relates to a nucleic acid, encoding thepeptides according to the present invention. The present inventionfurther relates to the nucleic acid according to the present inventionthat is DNA, cDNA, PNA, RNA or combinations thereof.

The present invention further relates to an expression vector capable ofexpressing and/or expressing a nucleic acid according to the presentinvention.

The present invention further relates to a peptide according to thepresent invention, a nucleic acid according to the present invention oran expression vector according to the present invention for use in thetreatment of diseases and in medicine, in particular in the treatment ofcancer.

The present invention further relates to antibodies that are specificagainst the peptides according to the present invention or complexes ofsaid peptides according to the present invention with MHC, and methodsof making these.

The present invention further relates to T-cell receptors (TCRs), inparticular soluble TCR (sTCRs) and cloned TCRs engineered intoautologous or allogeneic T cells, and methods of making these, as wellas NK cells or other cells bearing said TCR or cross-reacting with saidTCRs.

The antibodies and TCRs are additional embodiments of theimmunotherapeutic use of the peptides according to the invention athand.

The present invention further relates to a host cell comprising anucleic acid according to the present invention or an expression vectoras described before. The present invention further relates to the hostcell according to the present invention that is an antigen presentingcell, and preferably is a dendritic cell.

The present invention further relates to a method for producing apeptide according to the present invention, said method comprisingculturing the host cell according to the present invention, andisolating the peptide from said host cell or its culture medium.

The present invention further relates to said method according to thepresent invention, wherein the antigen is loaded onto class I or II MHCmolecules expressed on the surface of a suitable antigen-presenting cellor artificial antigen-presenting cell by contacting a sufficient amountof the antigen with an antigen-presenting cell.

The present invention further relates to the method according to thepresent invention, wherein the antigen-presenting cell comprises anexpression vector capable of expressing or expressing said peptidecontaining SEQ ID No. 1 to SEQ ID No.: 48, preferably containing SEQ IDNo: 1 to SEQ ID No: 6 (see Table 1) and SEQ ID No: 24 to SEQ ID No: 28(see Table 2), or a variant amino acid sequence.

The present invention further relates to activated T cells, produced bythe method according to the present invention, wherein said T cellselectively recognizes a cell which expresses a polypeptide comprisingan amino acid sequence according to the present invention.

The present invention further relates to a method of killing targetcells in a patient which target cells aberrantly express a polypeptidecomprising any amino acid sequence according to the present invention,the method comprising administering to the patient an effective numberof T cells as produced according to the present invention.

The present invention further relates to the use of any peptide asdescribed, the nucleic acid according to the present invention, theexpression vector according to the present invention, the cell accordingto the present invention, the activated T lymphocyte, the T cellreceptor or the antibody or other peptide- and/or peptide-MHC-bindingmolecules according to the present invention as a medicament or in themanufacture of a medicament. Preferably, said medicament is activeagainst cancer.

Preferably, said medicament is a cellular therapy, a vaccine or aprotein based on a soluble TCR or antibody.

The present invention further relates to a use according to the presentinvention, wherein said cancer cells are lung cancer, small cell lungcancer, melanoma, liver cancer, breast cancer, Uterine cancer, Merkelcell carcinoma, pancreatic cancer, gallbladder cancer, bile duct cancer,CRC, urinary bladder cancer, non-small cell lung cancer, kidney cancer,leukemia (e.g. AML or CLL), ovarian cancer, esophageal cancer, braincancer, and gastric (stomach) cancer, and most preferably prostatecancer cells.

The present invention further relates to biomarkers based on thepeptides according to the present invention, herein called “targets”,that can be used in the diagnosis of cancer, preferably prostate cancer.The marker can be over-presentation of the peptide(s) themselves, orover-expression of the corresponding gene(s). The markers may also beused to predict the probability of success of a treatment, preferably animmunotherapy, and most preferred an immunotherapy targeting the sametarget that is identified by the biomarker. For example, an antibody orsoluble TCR can be used to stain sections of the tumor to detect thepresence of a peptide of interest in complex with MHC.

Optionally, the antibody carries a further effector function such as animmune stimulating domain or toxin.

The present invention also relates to the use of these novel targets inthe context of cancer treatment.

Both therapeutic and diagnostic uses against additional cancerousdiseases are disclosed in the following more detailed description of theunderlying expression products (polypeptides) of the peptides accordingto the invention.

ATP-binding cassette, sub-family C (CFTR/MRP), member 4 (ABCC4)—ABCC4 iscapable of pumping a wide variety of endogenous and xenobiotic organicanionic compounds out of the cell, including a wide variety ofantiviral, cytostatic, antibiotic and cardiovascular drugs as well asmolecules involved in cellular signaling, thus giving ABCC4 a keyfunction in cellular protection and extracellular signaling pathways(Russel et al., 2008). ABCC4 levels are elevated in prostate cancer, andexpression has been shown to be regulated by androgen treatment invitro. Consequently, androgen ablation treatment lowers ABCC4 expressionin prostate cancer tissue. Moreover, ABCC4 levels decrease upon prostatecancer progression (Ho et al., 2008; Montani et al., 2013). ABCC4overexpression has also been demonstrated for other cancer types, as forexample in lung cancer (Zhao et al., 2014). Suppression of ABCC4expression was shown to inhibit proliferation of ABCC4-overexpressingcancer cells in vitro (Zhao et al., 2014) and to restore sensitivity tochemotherapeutics in drug-resistant cell lines (Zhang et al., 2014).

Astrotactin 2 (ASTN2)—ASTN2 is suggested to function in neuronal cellmigration (Wilson et al., 2010).

Alpha-2-glycoprotein 1, zinc-binding (AZGP1)—ASTN2 stimulates lipiddegradation in adipocytes and causes the extensive fat losses associatedwith some advanced cancers (UniProt, 2015). AZGP1 expression isincreased in prostate cancer, which is detectable also in serum samplesand has been suggested as potential biomarker (Hale et al., 2001).Levels decrease in high-grade tumors, and AZGP1 expression has beenassociated with decreased mortality and decreased tumor recurrence inprostate cancer patients (Lapointe et al., 2004; Severi et al., 2014).AZGP1 has been suggested as a biomarker for breast cancer, and AZGP1levels decrease in poorly differentiated tumors (Hassan et al., 2008).

Chromosome 6 open reading frame 132 (C6orf132)—C6orf132 is located onchromosome 6p21.1 (RefSeq, 2002).

CDKN1A interacting zinc finger protein 1 (CIZ1)—CIZ1 encodes for theCDKN1A interacting zinc finger protein which functions as a tumorsuppressor (Nishibe et al., 2013). In colorectal cancer CIZ1 wassuggested to be involved in cancer progression by regulating cellproliferation, cell cycle, apoptosis and colony formation (Yin et al.,2013). A CIZ1 variant that lacks part of the C-terminal domain is foundin lung cancer cells even at an early stage and has potential as abiomarker (Higgins et al., 2012).

Crystallin, mu (CRYM)—CRYM specifically catalyzes the reduction of iminebonds (Hallen et al., 2011). CRYM is an androgen-regulated gene whoseexpression is elevated in prostate cancer but down-regulated incastration therapy-resistant tumors (Malinowska et al., 2009). CRYM wasoverexpressed in non-small cell lung cancer and in metastasis of uterineleiomyosarcoma as compared to the primary tumor (Chong et al., 2006;Davidson et al., 2014). CRYM expression was also found in breast cancersamples, and CRYM was recognized by breast cancer patients' sera inSEREX analysis (Forti et al., 2002).

Cysteine and glycine-rich protein 2 (CSRP2)—CSRP2 belongs to the familyof CSRP genes, encoding LIM domain containing proteins. Over-expressionof CSRP2 is associated with de-differentiation of hepatocellularcarcinoma (Midorikawa et al., 2002).

Desmin (DES)—DES are class-III intermediate filaments found in musclecells. They form a fibrous network connecting myofibrils to each otherand to the plasma membrane from the periphery of the Z-line structures(Clemen et al., 2015). DES expression is decreased in prostate cancertissue and low DES expression has been associated with a shorterdisease-free period (Wu et al., 2014). In colorectal carcinoma, DESexpression was elevated in advanced stage tumors, possibly due toincreased microvessel density and thus increased levels of pericytes(Arentz et al., 2011). In addition, elevated DES levels have beenassociated with decreased survival in colorectal cancer (Ma et al.,2009).

Family with sequence similarity 129, member A (FAM129A)—FAM129A islocated on chromosome 1q25 (RefSeq, 2002). Overexpression of FAM129A hasbeen demonstrated in head and neck squamous cell carcinoma (Ito et al.,2010a), thyroid tumors (Matsumoto et al., 2006), and renal cellcarcinoma (Adachi et al., 2004).

FK506 binding protein 10 (FKBP10)—FKBP10 encodes the FK506 bindingprotein 10, which belongs to the FKBP-type peptidyl-prolyl cis/transisomerase family. The FKBP10 gene product localizes to the endoplasmicreticulum and acts as a molecular chaperone (RefSeq, 2002). FKBP10 wasidentified as a novel gene that participates in the acquisition andmaintenance of the adriamycin-resistant phenotype in leukemia cells (Sunet al., 2014). FKBP10 has been associated with colorectal cancer throughits up-regulation (Olesen et al., 2005). In contrast, theunder-expression of FKBP10 was characteristic for epithelial ovariancarcinomas (Quinn et al., 2013).

GATA binding protein 2 (GATA2)—GATA2 is critically required forhematopoiesis, and mutations in GATA2 are associated withmyelodysplastic syndrome and myeloid leukemia (Bresnick et al., 2012).In solid tumors, overexpression of GATA2 has been described in breastcancer and was correlated with poor prognosis in colorectal carcinomaand glioblastoma (Chen et al., 2013; Wang et al., 2015; Wang et al.,2012). In contrast, other reports rather suggest decreased expression ofGATA2 in neoplastic tissue and report an association of GATA2 reductionwith tumor aggressiveness and poor outcome in hepatocellular carcinoma,bladder cancer, or renal cell carcinoma (Kandimalla et al., 2012; Peterset al., 2014; Li et al., 2014).

Growth regulation by estrogen in breast cancer (GREB1)—GREB1 is anestrogen-responsive gene that is an early response gene in the estrogenreceptor-regulated pathway. It is thought to play an important role inhormone-responsive tissues and cancer (RefSeq, 2002). GREB1 isoverexpressed in prostate cancer and benign prostate hyperplasia, and isinvolved in androgen-induced growth of prostate cancer cells (Rae etal., 2006). GREB1 also mediates estrogen-stimulated proliferation ofovarian cancer and breast cancer cells (Laviolette et al., 2014).

Integrin alpha 7 (ITGA7)—ITGA7 is the alpha chain of the laminin-1receptor dimer integrin alpha-7/beta-1. ITGA7 is a tumor-suppressor genethat is critical for suppressing the growth of malignant tumors.Mutational analysis revealed ITGA7 mutations in prostate cancer,hepatocellular carcinoma, soft tissue leiomyosarcoma, and glioblastomamultiforme. ITGA7 was down-regulated in non-metastatic prostate cancerand leiomyosarcoma (Tan et al., 2013).

Potassium voltage-gated channel, subfamily G, member 1 (KCNG1)—KCNG1 isabundantly expressed in skeletal muscle (Gutman et al., 2005).

KIAA1244—KIAA1244 encodes for ARFGEF family member 3 and is located onchromosome 6q23.3. (RefSeq, 2002). KIAA1244 was found to beoverexpressed in a majority of breast cancers (Nishidate et al., 2004).

Kinesin family member 7 (KIF7)—KIF7 is implicated in a variety ofdiseases including Joubert, hydrolethalus and acrocallosal syndromes. Itis also involved in primary cilium formation (Klejnot and Kozielski,2012). Aberrant activation of Hedgehog signaling pathway, in which KIF7plays an important role, leads to pathological consequences in a varietyof human tumors, such as basal cell carcinoma of the skin, gastriccancer and pancreatic cancer (Li et al., 2012; Katoh and Katoh, 2005).

Kallikrein-related peptidase 4 (KLK4)—KLK4 is one of the fifteenkallikrein subfamily members whose genes are located in a cluster onchromosome 19 (Hu et al., 2000). KLK4 is elevated in breast cancer,ovarian cancer and prostate cancer (Schmitt et al., 2013). In prostatecancer KLK4 interacts with androgen and mTOR signaling (Jin et al.,2013).

Lactotransferrin (LTF)—LTF is a multifunctional protein that is found athighest levels in milk, and at lower concentrations in other mucosalfluids. LTF has been shown to exert antimicrobial and anti-inflammatoryactivity, is involved in iron homeostasis, and plays a role in cellgrowth and differentiation and in protection against cancer developmentand metastasis (Ward et al., 2005). LTF is downregulated in prostatecancer tissue and sera as compared to benign prostate hyperplasia. Inaddition, lowered LTF levels have been correlated with decreased patientsurvival (Shaheduzzaman et al., 2007). LTF inhibits cell growth byblocking cell cycle progression, possibly through several mechanisms,including inhibition of NF-kappaB and Akt signaling (Deng et al., 2013;Ye et al., 2014). In addition, LTF also exerts pro-apoptotic effects,including activation of caspase-3 and JNK signaling (Sakai et al., 2005;Wang et al., 2011).

Leucine-zipper-like transcription regulator 1 (LZTR1)—LZTR1 might play arole in regulation of the Ras/MAPK pathway (Yamamoto et al., 2015).LZTR1 is frequently mutated or deleted in glioblastoma (Frattini et al.,2013).

MANSC domain containing 1 (MANSC1)—MANSC1 is located on chromosome12p13.2 (RefSeq, 2002). MANSC1 was significantly downregulated inprostate tumors; it may be critical to initiation or progression ofprostate carcinoma (Kibel et al., 2004). In patients with differenthematologic malignancies MANSC1 shows an increased expression (Haferlachet al., 2011).

Microtubule-associated protein 1B (MAP1B)—MAP1B is amicrotubule-stabilizing protein which plays an important role in centralnervous system development and axon function (Halpain and Dehmelt,2006). Immunohistochemical analysis of childhood small round cell tumorssuggested that MAP1B is expressed in neuroblastoma, rhabdomyosarcoma,and Wilms tumor, but not in Ewing sarcoma (Willoughby et al., 2008)

Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) MAP4K4is a member of the serine/threonine protein kinase family and mediatethe TNF-alpha signaling pathway (RefSeq, 2002). MAP4K4 has beensuggested as a biomarker of prostate cancer aggressiveness (Rizzardi etal., 2014).

Misshapen-like kinase 1 (MINK1)—MINK1 regulates cytoskeletalorganization and oncogene-induced cell senescence. It is essential forcytokinesis (Hyodo et al., 2012). MINK1 is activated by Ras and mediatesp38 activation during growth arrest and senescence (Nicke et al., 2005).

Mohawk homeobox (MKX)—MKX is a transcription factor with a reported rolein development of bone, skeletal muscle and cartilage structures (Ito etal., 2010b).

Myosin, heavy chain 11, smooth muscle (MYH11)—MYH11 is assigned tochromosome region 16q12 and is expressed in the human umbilical artery,bladder, esophagus and trachea (Matsuoka et al., 1993). Inversion at theMYH11 chromosomal locus (inv(16); CBFB-MYH11) is frequently found inacute myeloid leukemia, leading to formation of an oncogenic chimericprotein of core binding factor (CBF-beta) and MYH11 (Liu et al., 1993).Low MYH11 expression levels were linked to poor prognosis in colorectalcancer (Wang et al., 2014).

Neurofilament, heavy polypeptide (NEFH)—Neurofilaments are type IVintermediate filament heteropolymers composed of light, medium, andheavy chains. Neurofilaments comprise the axoskeleton and functionallymaintain neuronal caliber. They may also play a role in intracellulartransport to axons and dendrites. NEFH encodes the heavy neurofilamentprotein (RefSeq, 2002). In patients with metastatic renal cellcarcinoma, NEFH CpG island methylation demonstrated a tumor-specificincrease, association with advanced disease and distant metastasis andwas significantly associated with a poor progression-free survival andreduced overall survival (Dubrowinskaja et al., 2014).

Olfactory receptor, family 51, subfamily E, member 2 (OR51E2)—OR51E2 isa member of the G-protein-coupled olfactory receptor family that ispredominantly expressed in the human prostate and often over-expressedin prostate cancer (Weng et al., 2005).

OR51E2-derived peptides may be used as diagnostic markers as well asimmune targets for development of anticancer vaccines (Matsueda et al.,2012).

Phosphodiesterase 11A (PDE11A)—PDE11A catalyzes the hydrolysis of cAMPand cGMP, thus downregulating the respective signaling pathways (Fawcettet al., 2000). Mutations in PDE11A have been associated withadrenocortical hyperplasia as well as with familial testicular germ celltumors (Greene et al., 2010; Horvath and Stratakis, 2008). One study hasalso identified missense mutations in PDE11A in 30% of prostate cancerpatients. The variants were characterized as displaying reduced PDE11Aactivity in vitro, and their expression levels in vivo were reduced(Faucz et al., 2011).

Plectin (PLEC)—PLEC encodes the plakin family member plectin, a proteininvolved in the cross-linking and organization of the cytoskeleton andadhesion complexes (Bouameur et al., 2014). PLEC is over-expressed incolorectal adenocarcinoma, head and neck squamous cell carcinoma andpancreatic cancer (Lee et al., 2004; Katada et al., 2012; Bausch et al.,2011).

PR domain containing 8 (PRDM8)—PRDM8 is a transcriptional repressor withhistone methyltransferase activity. PRDM8 is regulated by the Notch-Hespathway and plays a role in CNS development (Kinameri et al., 2008)

RAB3B, member RAS oncogene family (RAB3B)—RAB3B is a low molecularweight GTP-binding protein that has been implicated in the regulation ofexocytosis (Rotondo et al., 2009). RAB3B is overexpressed in prostatecancer patients, suggesting that RAB3B together with AR, FoxA1, andNKX3-1 are important regulators of prostate cancer progression (Tan etal., 2012).

Solute carrier family 39 (zinc transporter), member 6 (SLC39A6)—SLC39A6codes for the Zinc transporter ZIP6, an effector molecule downstream ofsoluble growth factors (Lue et al., 2011). In breast cancerover-expression of SLC39A6 is associated with shorter recurrence timesas well as reduced time to disease-related mortality (Andres et al.,2013).

Six transmembrane epithelial antigen of the prostate 2 (STEAP2)—STEAP2encodes a multi-pass membrane protein that localizes to the Golgicomplex, the plasma membrane, and the vesicular tubular structures inthe cytosol (RefSeq, 2002). STEAP2 expression is elevated in prostatecancer patients with advanced disease. Overexpression of STEAP2 has beendemonstrated to increase cell proliferation as well as migratory andinvasive potential in vitro, while knock-down inhibited cell growth andmight promote apoptosis (Wang et al., 2010; Whiteland et al., 2014).Together with other members of the STEAP protein family, STEAP2 is alsooverexpressed in other cancer types. In addition, STEAPs have beeninvestigated as cancer biomarkers and potential targets for cancerimmunotherapy (Grunewald et al., 2012).

Synemin, intermediate filament protein (SYNM)—SYNM links desmin with theextracellular matrix and plays an important structural role in muscle(Bhosle et al., 2006). SYNM expression was downregulated in breastcancer and hepatocellular carcinoma, which correlated with decreasedsurvival, lymph node metastases and advanced grade (Noetzel et al.,2010; Liu et al., 2011).

Synaptopodin 2 (SYNPO2)—SYNPO2, also known as myopodin, is anactin-binding protein that plays a role in regulating cell migration inresponse to chemotactic stimuli (Kai et al., 2015). SYNPO2 is considereda tumor-suppressor gene and absence of SYNPO2 in prostate cancer hasbeen correlated with invasiveness and clinical relapse (Yu et al.,2006).

Transforming growth factor, beta 3 (TGFB3)—TGFB3 is one of at leastthree isoforms of TGF-beta. In normal cells, TGF-beta signaling stopsthe cell cycle at the G1 stage to stop proliferation, inducedifferentiation, or promote apoptosis (Hanahan and Weinberg, 2000). InNSCLC TGFB3 is a pro-invasive factor (Petrella et al., 2012)

TRAF2 and NCK interacting kinase (TNIK)—TNIK is a germinal center kinaseand is potentially involved in regulation of the actin cytoskeleton (Fuet al., 1999). TNIK is an essential, specific activator of Wnt targetgenes. TNIK was described as a key player in TRAF6-dependent JNK andNF-kappaB signaling and a transducer of activating and transformingsignals in human B-cells (Shkoda et al., 2012) In hormone receptornegative breast cancer, TNIK was identified as a potential cancer genewith impact on growth and proliferation (Jiao et al., 2013)

Tryptase alpha/beta 1 (TPSAB1), Tryptase beta 2 (TPSAB2)—TPSAB1 andTPSAB2 are both serine proteases which are mainly expressed by mastcells. The presence of tryptase-positive mast cells in tumor tissuecorrelates with angiogenesis in several cancer types, includingmelanoma, endometrial carcinoma, breast cancer, gastric cancer andcolorectal cancer (Ammendola et al., 2014).

Transient receptor potential cation channel, subfamily M, member 8(TRPM8)—TRPM8 is a sodium and calcium channel which is activated inresponse to cold stimuli. TRPM8 is expressed primarily in prostateepithelial cells, and in addition also in some sensory neurons(Prevarskaya et al., 2007). TRPM8 is reported to be overexpressed inprostate cancer and other cancer types, such as breast, colon, lung andskin tumors (Tsavaler et al., 2001).

Thioredoxin domain containing 16 (TXNDC16)—TXNDC16 encodes a protein of858 amino acids with a putative thioredoxin 2 domain; it's function isunknown. Autoantibodies against TXNDC16 have been detected in meningiomapatients (Comtesse et al., 2005).

Unc-13 homolog B (UNC13B)—UNC13B is a constituent of a protein complexat the presynaptic active zone that controls neurotransmitter release bysynaptic vesicle exocytosis (Sudhof, 2012).

Zinc finger protein 426 (ZNF426)—ZNF426 is a transcription regulatoryprotein (Yang and Wood, 2007).

DETAILED DESCRIPTION OF THE INVENTION

Stimulation of an immune response is dependent upon the presence ofantigens recognized as foreign by the host immune system. The discoveryof the existence of tumor associated antigens has raised the possibilityof using a host's immune system to intervene in tumor growth. Variousmechanisms of harnessing both the humoral and cellular arms of theimmune system are currently being explored for cancer immunotherapy.

Specific elements of the cellular immune response are capable ofspecifically recognizing and destroying tumor cells. The isolation ofT-cells from tumor-infiltrating cell populations or from peripheralblood suggests that such cells play an important role in natural immunedefense against cancer. CD8-positive T-cells in particular, whichrecognize class I molecules of the major histocompatibility complex(MHC)-bearing peptides of usually 8 to 10 amino acid residues derivedfrom proteins or defect ribosomal products (DRIPS) located in thecytosol, play an important role in this response. The MHC-molecules ofthe human are also designated as human leukocyte-antigens (HLA).

As used herein and except as noted otherwise all terms are defined asgiven below.

The term “T-cell response” means the specific proliferation andactivation of effector functions induced by a peptide in vitro or invivo. For MHC class I restricted cytotoxic T cells, effector functionsmay be lysis of peptide-pulsed, peptide-precursor pulsed or naturallypeptide-presenting target cells, secretion of cytokines, preferablyInterferon-gamma, TNF-alpha, or IL-2 induced by peptide, secretion ofeffector molecules, preferably granzymes or perforins induced bypeptide, or degranulation.

The term “peptide” is used herein to designate a series of amino acidresidues, connected one to the other typically by peptide bonds betweenthe alpha-amino and carbonyl groups of the adjacent amino acids. Thepeptides are preferably 9 amino acids in length, but can be as short as8 amino acids in length, and as long as 10, 11, 12, or 13 or longer, andin case of MHC class II peptides (elongated variants of the peptides ofthe invention) they can be as long as 14, 15, 16, 17, 18, 19 or 20 ormore amino acids in length.

Furthermore, the term “peptide” shall include salts of a series of aminoacid residues, connected one to the other typically by peptide bondsbetween the alpha-amino and carbonyl groups of the adjacent amino acids.Preferably, the salts are pharmaceutical acceptable salts of thepeptides, such as, for example, the chloride or acetate(trifluoroacetate) salts. It has to be noted that the salts of thepeptides according to the present invention differ substantially fromthe peptides in their state(s) in vivo, as the peptides are not salts invivo.

The term “peptide” shall also include “oligopeptide”. The term“oligopeptide” is used herein to designate a series of amino acidresidues, connected one to the other typically by peptide bonds betweenthe alpha-amino and carbonyl groups of the adjacent amino acids. Thelength of the oligopeptide is not critical to the invention, as long asthe correct epitope or epitopes are maintained therein. Theoligopeptides are typically less than about 30 amino acid residues inlength, and greater than about 15 amino acids in length.

The term “polypeptide” designates a series of amino acid residues,connected one to the other typically by peptide bonds between thealpha-amino and carbonyl groups of the adjacent amino acids. The lengthof the polypeptide is not critical to the invention as long as thecorrect epitopes are maintained. In contrast to the terms peptide oroligopeptide, the term polypeptide is meant to refer to moleculescontaining more than about 30 amino acid residues.

A peptide, oligopeptide, protein or polynucleotide coding for such amolecule is “immunogenic” (and thus is an “immunogen” within the presentinvention), if it is capable of inducing an immune response. In the caseof the present invention, immunogenicity is more specifically defined asthe ability to induce a T-cell response. Thus, an “immunogen” would be amolecule that is capable of inducing an immune response, and in the caseof the present invention, a molecule capable of inducing a T-cellresponse. In another aspect, the immunogen can be the peptide, thecomplex of the peptide with MHC, oligopeptide, and/or protein that isused to raise specific antibodies or TCRs against it.

A class I T cell “epitope” requires a short peptide that is bound to aclass I MHC receptor, forming a ternary complex (MHC class I alphachain, beta-2-microglobulin, and peptide) that can be recognized by a Tcell bearing a matching T-cell receptor binding to the MHC/peptidecomplex with appropriate affinity. Peptides binding to MHC class Imolecules are typically 8-14 amino acids in length, and most typically 9amino acids in length.

In humans there are three different genetic loci that encode MHC class Imolecules (the MHC-molecules of the human are also designated humanleukocyte antigens (HLA)): HLA-A, HLA-B, and HLA-C. HLA-A*01, HLA-A*02,and HLA-B*07 are examples of different MHC class I alleles that can beexpressed from these loci.

TABLE 8 Expression frequencies F of HLA-A*02 and HLA-A*24 and the mostfrequent HLA-DR serotypes. Frequencies are deduced from haplotypefrequencies Gf within the American population adapted from Mori et al.(Mori et al., 1997) employing the Hardy-Weinberg formula F = 1 − (1 −Gf)². Combinations of A*02 or A*24 with certain HLA-DR alleles might beenriched or less frequent than expected from their single frequenciesdue to linkage disequilibrium. For details refer to Chanock et al.(Chanock et al., 2004). Calculated phenotype Allele Population fromallele frequency A*02 Caucasian (North America)  49.1% A*02 AfricanAmerican (North America)  34.1% A*02 Asian American (North America) 43.2% A*02 Latin American (North American)  48.3% DR1 Caucasian (NorthAmerica)  19.4% DR2 Caucasian (North America)  28.2% DR3 Caucasian(North America)  20.6% DR4 Caucasian (North America)  30.7% DR5Caucasian (North America)  23.3% DR6 Caucasian (North America)  26.7%DR7 Caucasian (North America)  24.8% DR8 Caucasian (North America)  5.7%DR9 Caucasian (North America)  2.1% DR1 African (North) American 13.20%DR2 African (North) American 29.80% DR3 African (North) American 24.80%DR4 African (North) American 11.10% DR5 African (North) American 31.10%DR6 African (North) American 33.70% DR7 African (North) American 19.20%DR8 African (North) American 12.10% DR9 African (North) American  5.80%DR1 Asian (North) American  6.80% DR2 Asian (North) American 33.80% DR3Asian (North) American  9.20% DR4 Asian (North) American 28.60% DR5Asian (North) American 30.00% DR6 Asian (North) American 25.10% DR7Asian (North) American 13.40% DR8 Asian (North) American 12.70% DR9Asian (North) American 18.60% DR1 Latin (North) American 15.30% DR2Latin (North) American 21.20% DR3 Latin (North) American 15.20% DR4Latin (North) American 36.80% DR5 Latin (North) American 20.00% DR6Latin (North) American 31.10% DR7 Latin (North) American 20.20% DR8Latin (North) American 18.60% DR9 Latin (North) American  2.10% A*24Philippines   65% A*24 Russia Nenets   61% A*24:02 Japan   59% A*24Malaysia   58% A*24:02 Philippines   54% A*24 India   47% A*24 SouthKorea   40% A*24 Sri Lanka   37% A*24 China   32% A*24:02 India   29%A*24 Australia West   22% A*24 USA   22% A*24 Russia Samara   20% A*24South America   20% A*24 Europe   18%

The peptides of the invention, preferably when included into a vaccineof the invention as described herein bind to HLA-A*02 or HLA-A*24. Avaccine may also include pan-binding MHC class II peptides. Therefore,the vaccine of the invention can be used to treat cancer in patientsthat are A*02 positive, whereas no selection for MHC class II allotypesis necessary due to the pan-binding nature of these peptides.

If A*02 peptides of the invention are combined with peptides binding toanother allele, for example A*24, a higher percentage of any patientpopulation can be treated compared with addressing either MHC class Iallele alone. While in most populations less than 50% of patients couldbe addressed by either allele alone, a vaccine comprising HLA-A*24 andHLA-A*02 epitopes can treat at least 60% of patients in any relevantpopulation. Specifically, the following percentages of patients will bepositive for at least one of these alleles in various regions: USA 61%,Western Europe 62%, China 75%, South Korea 77%, Japan 86%.

In a preferred embodiment, the term “nucleotide sequence” refers to aheteropolymer of deoxyribonucleotides.

The nucleotide sequence coding for a particular peptide, oligopeptide,or polypeptide may be naturally occurring or they may be syntheticallyconstructed. Generally, DNA segments encoding the peptides,polypeptides, and proteins of this invention are assembled from cDNAfragments and short oligonucleotide linkers, or from a series ofoligonucleotides, to provide a synthetic gene that is capable of beingexpressed in a recombinant transcriptional unit comprising regulatoryelements derived from a microbial or viral operon.

As used herein the term “a nucleotide coding for (or encoding) apeptide” refers to a nucleotide sequence coding for the peptideincluding artificial (man-made) start and stop codons compatible for thebiological system the sequence is to be expressed by, for example, adendritic cell or another cell system useful for the production of TCRs.

As used herein, reference to a nucleic acid sequence includes bothsingle stranded and double stranded nucleic acid. Thus, for example forDNA, the specific sequence, unless the context indicates otherwise,refers to the single strand DNA of such sequence, the duplex of suchsequence with its complement (double stranded DNA) and the complement ofsuch sequence.

The term “coding region” refers to that portion of a gene which eithernaturally or normally codes for the expression product of that gene inits natural genomic environment, i.e., the region coding in vivo for thenative expression product of the gene.

The coding region can be derived from a non-mutated (“normal”), mutatedor altered gene, or can even be derived from a DNA sequence, or gene,wholly synthesized in the laboratory using methods well known to thoseof skill in the art of DNA synthesis.

The term “expression product” means the polypeptide or protein that isthe natural translation product of the gene and any nucleic acidsequence coding equivalents resulting from genetic code degeneracy andthus coding for the same amino acid(s).

The term “fragment”, when referring to a coding sequence, means aportion of DNA comprising less than the complete coding region, whoseexpression product retains essentially the same biological function oractivity as the expression product of the complete coding region.

The term “DNA segment” refers to a DNA polymer, in the form of aseparate fragment or as a component of a larger DNA construct, which hasbeen derived from DNA isolated at least once in substantially pure form,i.e., free of contaminating endogenous materials and in a quantity orconcentration enabling identification, manipulation, and recovery of thesegment and its component nucleotide sequences by standard bio-chemicalmethods, for example, by using a cloning vector. Such segments areprovided in the form of an open reading frame uninterrupted by internalnon-translated sequences, or introns, which are typically present ineukaryotic genes. Sequences of non-translated DNA may be presentdownstream from the open reading frame, where the same do not interferewith manipulation or expression of the coding regions.

The term “primer” means a short nucleic acid sequence that can be pairedwith one strand of DNA and provides a free 3′-OH end at which a DNApolymerase starts synthesis of a deoxyribonucleotide chain.

The term “promoter” means a region of DNA involved in binding of RNApolymerase to initiate transcription.

The term “isolated” means that the material is removed from its originalenvironment (e.g., the natural environment, if it is naturallyoccurring). For example, a naturally-occurring polynucleotide orpolypeptide present in a living animal is not isolated, but the samepolynucleotide or polypeptide, separated from some or all of thecoexisting materials in the natural system, is isolated. Suchpolynucleotides could be part of a vector and/or such polynucleotides orpolypeptides could be part of a composition, and still be isolated inthat such vector or composition is not part of its natural environment.

The polynucleotides, and recombinant or immunogenic polypeptides,disclosed in accordance with the present invention may also be in“purified” form. The term “purified” does not require absolute purity;rather, it is intended as a relative definition, and can includepreparations that are highly purified or preparations that are onlypartially purified, as those terms are understood by those of skill inthe relevant art. For example, individual clones isolated from a cDNAlibrary have been conventionally purified to electrophoretichomogeneity. Purification of starting material or natural material to atleast one order of magnitude, preferably two or three orders, and morepreferably four or five orders of magnitude is expressly contemplated.Furthermore, a claimed polypeptide which has a purity of preferably99.999%, or at least 99.99% or 99.9%; and even desirably 99% by weightor greater is expressly encompassed.

The nucleic acids and polypeptide expression products disclosedaccording to the present invention, as well as expression vectorscontaining such nucleic acids and/or such polypeptides, may be in“enriched form”. As used herein, the term “enriched” means that theconcentration of the material is at least about 2, 5, 10, 100, or 1000times its natural concentration (for example), advantageously 0.01%, byweight, preferably at least about 0.1% by weight. Enriched preparationsof about 0.5%, 1%, 5%, 10%, and 20% by weight are also contemplated. Thesequences, constructs, vectors, clones, and other materials comprisingthe present invention can advantageously be in enriched or isolatedform. The term “active fragment” means a fragment, usually of a peptide,polypeptide or nucleic acid sequence, that generates an immune response(i.e., has immunogenic activity) when administered, alone or optionallywith a suitable adjuvant or in a vector, to an animal, such as a mammal,for example, a rabbit or a mouse, and also including a human, suchimmune response taking the form of stimulating a T-cell response withinthe recipient animal, such as a human. Alternatively, the “activefragment” may also be used to induce a T-cell response in vitro.

As used herein, the terms “portion”, “segment” and “fragment”, when usedin relation to polypeptides, refer to a continuous sequence of residues,such as amino acid residues, which sequence forms a subset of a largersequence. For example, if a polypeptide were subjected to treatment withany of the common endopeptidases, such as trypsin or chymotrypsin, theoligopeptides resulting from such treatment would represent portions,segments or fragments of the starting polypeptide. When used in relationto polynucleotides, these terms refer to the products produced bytreatment of said polynucleotides with any of the endonucleases.

In accordance with the present invention, the term “percent identity” or“percent identical”, when referring to a sequence, means that a sequenceis compared to a claimed or described sequence after alignment of thesequence to be compared (the “Compared Sequence”) with the described orclaimed sequence (the “Reference Sequence”). The percent identity isthen determined according to the following formula:percent identity=100[1−(C/R)]wherein C is the number of differences between the Reference Sequenceand the Compared Sequence over the length of alignment between theReference Sequence and the Compared Sequence, wherein

-   (i) each base or amino acid in the Reference Sequence that does not    have a corresponding aligned base or amino acid in the Compared    Sequence and-   (ii) each gap in the Reference Sequence and-   (iii) each aligned base or amino acid in the Reference Sequence that    is different from an aligned base or amino acid in the Compared    Sequence, constitutes a difference and-   (iiii) the alignment has to start at position 1 of the aligned    sequences;    and R is the number of bases or amino acids in the Reference    Sequence over the length of the alignment with the Compared Sequence    with any gap created in the Reference Sequence also being counted as    a base or amino acid.

If an alignment exists between the Compared Sequence and the ReferenceSequence for which the percent identity as calculated above is aboutequal to or greater than a specified minimum Percent Identity then theCompared Sequence has the specified minimum percent identity to theReference Sequence even though alignments may exist in which the hereinabove calculated percent identity is less than the specified percentidentity.

As mentioned above, the present invention thus provides a peptidecomprising a sequence that is selected from the group of consisting ofSEQ ID No: 1 to SEQ ID No: 48 or a variant thereof which is 88%homologous to SEQ ID No: 1 to SEQ ID No: 48, or a variant thereof thatwill induce T cells cross-reacting with said peptide. The peptides ofthe invention have the ability to bind to a molecule of the human majorhistocompatibility complex (MHC) class-I or elongated versions of saidpeptides to class II.

In the present invention, the term “homologous” refers to the degree ofidentity (see percent identity above) between sequences of two aminoacid sequences, i.e. peptide or polypeptide sequences. Theaforementioned “homology” is determined by comparing two sequencesaligned under optimal conditions over the sequences to be compared. Sucha sequence homology can be calculated by creating an alignment using,for example, the ClustalW algorithm. Commonly available sequenceanalysis software, more specifically, Vector NTI, GENETYX or other toolsare provided by public databases.

A person skilled in the art will be able to assess, whether T cellsinduced by a variant of a specific peptide will be able to cross-reactwith the peptide itself (Appay et al., 2006; Colombetti et al., 2006;Fong et al., 2001; Zaremba et al., 1997).

By a “variant” of the given amino acid sequence the inventors mean thatthe side chains of, for example, one or two of the amino acid residuesare altered (for example by replacing them with the side chain ofanother naturally occurring amino acid residue or some other side chain)such that the peptide is still able to bind to an HLA molecule insubstantially the same way as a peptide consisting of the given aminoacid sequence in consisting of SEQ ID No: 1 to SEQ ID No: 48. Forexample, a peptide may be modified so that it at least maintains, if notimproves, the ability to interact with and bind to the binding groove ofa suitable MHC molecule, such as HLA-A*02 or -DR, and in that way it atleast maintains, if not improves, the ability to bind to the TCR ofactivated T cells.

These T cells can subsequently cross-react with cells and kill cellsthat express a polypeptide that contains the natural amino acid sequenceof the cognate peptide as defined in the aspects of the invention. Ascan be derived from the scientific literature and databases (Rammenseeet al., 1999; Godkin et al., 1997), certain positions of HLA bindingpeptides are typically anchor residues forming a core sequence fittingto the binding motif of the HLA receptor, which is defined by polar,electrophysical, hydrophobic and spatial properties of the polypeptidechains constituting the binding groove. Thus, one skilled in the artwould be able to modify the amino acid sequences set forth in SEQ ID No:1 to SEQ ID No: 48, by maintaining the known anchor residues, and wouldbe able to determine whether such variants maintain the ability to bindMHC class I or II molecules. The variants of the present inventionretain the ability to bind to the TCR of activated T cells, which cansubsequently cross-react with and kill cells that express a polypeptidecontaining the natural amino acid sequence of the cognate peptide asdefined in the aspects of the invention.

The original (unmodified) peptides as disclosed herein can be modifiedby the substitution of one or more residues at different, possiblyselective, sites within the peptide chain, if not otherwise stated.Preferably those substitutions are located at the end of the amino acidchain. Such substitutions may be of a conservative nature, for example,where one amino acid is replaced by an amino acid of similar structureand characteristics, such as where a hydrophobic amino acid is replacedby another hydrophobic amino acid. Even more conservative would bereplacement of amino acids of the same or similar size and chemicalnature, such as where leucine is replaced by isoleucine. In studies ofsequence variations in families of naturally occurring homologousproteins, certain amino acid substitutions are more often tolerated thanothers, and these are often show correlation with similarities in size,charge, polarity, and hydrophobicity between the original amino acid andits replacement, and such is the basis for defining “conservativesubstitutions.”

Conservative substitutions are herein defined as exchanges within one ofthe following five groups: Group 1-small aliphatic, nonpolar or slightlypolar residues (Ala, Ser, Thr, Pro, Gly); Group 2-polar, negativelycharged residues and their amides (Asp, Asn, Glu, Gln); Group 3-polar,positively charged residues (His, Arg, Lys); Group 4-large, aliphatic,nonpolar residues (Met, Leu, Ile, Val, Cys); and Group 5-large, aromaticresidues (Phe, Tyr, Trp).

Less conservative substitutions might involve the replacement of oneamino acid by another that has similar characteristics but is somewhatdifferent in size, such as replacement of an alanine by an isoleucineresidue. Highly non-conservative replacements might involve substitutingan acidic amino acid for one that is polar, or even for one that isbasic in character. Such “radical” substitutions cannot, however, bedismissed as potentially ineffective since chemical effects are nottotally predictable and radical substitutions might well give rise toserendipitous effects not otherwise predictable from simple chemicalprinciples.

Of course, such substitutions may involve structures other than thecommon L-amino acids. Thus, D-amino acids might be substituted for theL-amino acids commonly found in the antigenic peptides of the inventionand yet still be encompassed by the disclosure herein. In addition,non-standard amino acids (i.e., other than the common naturallyoccurring proteinogenic amino acids) may also be used for substitutionpurposes to produce immunogens and immunogenic polypeptides according tothe present invention.

If substitutions at more than one position are found to result in apeptide with substantially equivalent or greater antigenic activity asdefined below, then combinations of those substitutions will be testedto determine if the combined substitutions result in additive orsynergistic effects on the antigenicity of the peptide. At most, no morethan 4 positions within the peptide would be simultaneously substituted.

A peptide consisting essentially of the amino acid sequence as indicatedherein can have one or two non-anchor amino acids (see below regardingthe anchor motif) exchanged without that the ability to bind to amolecule of the human major histocompatibility complex (MHC) class-I or-II is substantially changed or is negatively affected, when compared tothe non-modified peptide. In another embodiment, in a peptide consistingessentially of the amino acid sequence as indicated herein, one or twoamino acids can be exchanged with their conservative exchange partners(see herein below) without that the ability to bind to a molecule of thehuman major histocompatibility complex (MHC) class-I or -II issubstantially changed, or is negatively affected, when compared to thenon-modified peptide.

The amino acid residues that do not substantially contribute tointeractions with the T-cell receptor can be modified by replacementwith other amino acids whose incorporation does not substantially affectT-cell reactivity and does not eliminate binding to the relevant MHC.Thus, apart from the proviso given, the peptide of the invention may beany peptide (by which term the inventors include oligopeptide orpolypeptide), which includes the amino acid sequences or a portion orvariant thereof as given.

TABLE 9 Variants and motif of the HLA-A*02 peptides according to SEQ IDNo: 2, 4, and 8 Position 1 2 3 4 5 6 7 8 9 SEQ ID No. 2 S M L G E E I QL Variants V I A L L V L I L A A A V A I A A V V V V I V A T T V T I T AQ Q V Q I Q A SEQ ID No 4 A L L T F V W K L Variants V I A M M V M I M AA A V A I A A V V V V I V A T T V T I T A Q Q V Q I Q A SEQ ID No. 8 L LD F S L A D A Variants I L V M M I M L M V A A I A L A V V V I V L V V TT I T L T V Q Q I Q L Q V

TABLE 10 Variants and motif of the HLA-A*24 peptides according to SEQ IDNo: 25, 30, and 34 Position 1 2 3 4 5 6 7 8 9 10 11 SEQ ID 25 I Y E P YL A M F Variant I L F F I F L SEQ ID 30 S Y S P A H A R L Variant I F FF I F F SEQ ID 34 A F S P D S H Y L L F Variant Y I Y L Y I L

Longer (elongated) peptides may also be suitable. It is possible thatMHC class I epitopes, although usually between 8 and 11 amino acidslong, are generated by peptide processing from longer peptides orproteins that include the actual epitope. It is preferred that theresidues that flank the actual epitope are residues that do notsubstantially affect proteolytic cleavage necessary to expose the actualepitope during processing.

The peptides of the invention can be elongated by up to four aminoacids, that is 1, 2, 3 or 4 amino acids can be added to either end inany combination between 4:0 and 0:4. Combinations of the elongationsaccording to the invention can be found in Table 11.

TABLE 11 Combinations of the elongations of peptides of the inventionC-terminus N-terminus 4 0 3 0 or 1 2 0 or 1 or 2 1 0 or 1 or 2 or 3 0 0or 1 or 2 or 3 or 4 N-terminus C-terminus 4 0 3 0 or 1 2 0 or 1 or 2 1 0or 1 or 2 or 3 0 0 or 1 or 2 or 3 or 4

The amino acids for the elongation/extension can be the peptides of theoriginal sequence of the protein or any other amino acid(s). Theelongation can be used to enhance the stability or solubility of thepeptides.

Thus, the epitopes of the present invention may be identical tonaturally occurring tumor-associated or tumor-specific epitopes or mayinclude epitopes that differ by no more than four residues from thereference peptide, as long as they have substantially identicalantigenic activity.

In an alternative embodiment, the peptide is elongated on either or bothsides by more than 4 amino acids, preferably to a total length of up to30 amino acids. This may lead to MHC class II binding peptides. Bindingto MHC class II can be tested by methods known in the art.

Accordingly, the present invention provides peptides and variants of MHCclass I epitopes, wherein the peptide or variant has an overall lengthof between 8 and 100, preferably between 8 and 30, and most preferredbetween 8 and 14, namely 8, 9, 10, 11, 12, 13, 14 amino acids, in caseof the elongated class II binding peptides the length can also be 15,16, 17, 18, 19, 20, 21 or 22 amino acids.

Of course, the peptide or variant according to the present inventionwill have the ability to bind to a molecule of the human majorhistocompatibility complex (MHC) class I or II. Binding of a peptide ora variant to a MHC complex may be tested by methods known in the art.

Preferably, when the T cells specific for a peptide according to thepresent invention are tested against the substituted peptides, thepeptide concentration at which the substituted peptides achieve half themaximal increase in lysis relative to background is no more than about 1mM, preferably no more than about 1 μM, more preferably no more thanabout 1 nM, and still more preferably no more than about 100 pM, andmost preferably no more than about 10 pM. It is also preferred that thesubstituted peptide be recognized by T cells from more than oneindividual, at least two, and more preferably three individuals.

In a particularly preferred embodiment of the invention the peptideconsists or consists essentially of an amino acid sequence according toSEQ ID No: 1 to SEQ ID No: 48.

“Consisting essentially of” shall mean that a peptide according to thepresent invention, in addition to the sequence according to any of SEQID No: 1 to SEQ ID No 48 or a variant thereof contains additional N-and/or C-terminally located stretches of amino acids that are notnecessarily forming part of the peptide that functions as an epitope forMHC molecules epitope.

Nevertheless, these stretches can be important to provide an efficientintroduction of the peptide according to the present invention into thecells. In one embodiment of the present invention, the peptide is partof a fusion protein which comprises, for example, the 80 N-terminalamino acids of the HLA-DR antigen-associated invariant chain (p33, inthe following “Ii”) as derived from the NCBI, GenBank Accession numberX00497. In other fusions, the peptides of the present invention can befused to an antibody as described herein, or a functional part thereof,in particular into a sequence of an antibody, so as to be specificallytargeted by said antibody, or, for example, to or into an antibody thatis specific for dendritic cells as described herein.

In addition, the peptide or variant may be modified further to improvestability and/or binding to MHC molecules in order to elicit a strongerimmune response. Methods for such an optimization of a peptide sequenceare well known in the art and include, for example, the introduction ofreverse peptide bonds or non-peptide bonds.

In a reverse peptide bond amino acid residues are not joined by peptide(—CO—NH—) linkages but the peptide bond is reversed. Such retro-inversopeptidomimetics may be made using methods known in the art, for examplesuch as those described in Meziere et al (1997) (Meziere et al., 1997),incorporated herein by reference. This approach involves makingpseudopeptides containing changes involving the backbone, and not theorientation of side chains. Meziere et al. (Meziere et al., 1997) showthat for MHC binding and T helper cell responses, these pseudopeptidesare useful. Retro-inverse peptides, which contain NH—CO bonds instead ofCO—NH peptide bonds, are much more resistant to proteolysis.

A non-peptide bond is, for example, —CH₂—NH, —CH₂S—, —CH₂CH₂—, —CH═CH—,—COCH₂—, —CH(OH)CH₂—, and —CH₂SO—. U.S. Pat. No. 4,897,445 provides amethod for the solid phase synthesis of non-peptide bonds (—CH₂—NH) inpolypeptide chains which involves polypeptides synthesized by standardprocedures and the non-peptide bond synthesized by reacting an aminoaldehyde and an amino acid in the presence of NaCNBH₃.

Peptides comprising the sequences described above may be synthesizedwith additional chemical groups present at their amino and/or carboxytermini, to enhance the stability, bioavailability, and/or affinity ofthe peptides. For example, hydrophobic groups such as carbobenzoxy,dansyl, or t-butyloxycarbonyl groups may be added to the peptides' aminotermini. Likewise, an acetyl group or a 9-fluorenylmethoxy-carbonylgroup may be placed at the peptides' amino termini. Additionally, thehydrophobic group, t-butyloxycarbonyl, or an amido group may be added tothe peptides' carboxy termini.

Further, the peptides of the invention may be synthesized to alter theirsteric configuration. For example, the D-isomer of one or more of theamino acid residues of the peptide may be used, rather than the usualL-isomer. Still further, at least one of the amino acid residues of thepeptides of the invention may be substituted by one of the well-knownnon-naturally occurring amino acid residues. Alterations such as thesemay serve to increase the stability, bioavailability and/or bindingaction of the peptides of the invention.

Similarly, a peptide or variant of the invention may be modifiedchemically by reacting specific amino acids either before or aftersynthesis of the peptide. Examples for such modifications are well knownin the art and are summarized e.g. in R. Lundblad, Chemical Reagents forProtein Modification, 3rd ed. CRC Press, 2004 (Lundblad, 2004), which isincorporated herein by reference. Chemical modification of amino acidsincludes but is not limited to, modification by acylation, amidination,pyridoxylation of lysine, reductive alkylation, trinitrobenzylation ofamino groups with 2,4,6-trinitrobenzene sulphonic acid (TNBS), amidemodification of carboxyl groups and sulphydryl modification by performicacid oxidation of cysteine to cysteic acid, formation of mercurialderivatives, formation of mixed disulphides with other thiol compounds,reaction with maleimide, carboxymethylation with iodoacetic acid oriodoacetamide and carbamoylation with cyanate at alkaline pH, althoughwithout limitation thereto. In this regard, the skilled person isreferred to Chapter 15 of Current Protocols In Protein Science, Eds.Coligan et al. (John Wiley and Sons NY 1995-2000) (Coligan et al., 1995)for more extensive methodology relating to chemical modification ofproteins.

Briefly, modification of e.g. arginyl residues in proteins is oftenbased on the reaction of vicinal dicarbonyl compounds such asphenylglyoxal, 2,3-butanedione, and 1,2-cyclohexanedione to form anadduct. Another example is the reaction of methylglyoxal with arginineresidues. Cysteine can be modified without concomitant modification ofother nucleophilic sites such as lysine and histidine. As a result, alarge number of reagents are available for the modification of cysteine.The websites of companies such as Sigma-Aldrich provide information onspecific reagents.

Selective reduction of disulfide bonds in proteins is also common.Disulfide bonds can be formed and oxidized during the heat treatment ofbiopharmaceuticals. Woodward's Reagent K may be used to modify specificglutamic acid residues. N-(3-(dimethylamino)propyl)-N′-ethylcarbodiimidecan be used to form intra-molecular crosslinks between a lysine residueand a glutamic acid residue. For example, diethylpyrocarbonate is areagent for the modification of histidyl residues in proteins. Histidinecan also be modified using 4-hydroxy-2-nonenal. The reaction of lysineresidues and other α-amino groups is, for example, useful in binding ofpeptides to surfaces or the cross-linking of proteins/peptides. Lysineis the site of attachment of poly(ethylene)glycol and the major site ofmodification in the glycosylation of proteins. Methionine residues inproteins can be modified with e.g. iodoacetamide, bromoethylamine, andchloramine T.

Tetranitromethane and N-acetylimidazole can be used for the modificationof tyrosyl residues. Cross-linking via the formation of dityrosine canbe accomplished with hydrogen peroxide/copper ions.

Recent studies on the modification of tryptophan have usedN-bromosuccinimide, 2-hydroxy-5-nitrobenzyl bromide or3-bromo-3-methyl-2-(2-nitrophenylmercapto)-3H-indole (BPNS-skatole).

Successful modification of therapeutic proteins and peptides with PEG isoften associated with an extension of circulatory half-life whilecross-linking of proteins with glutaraldehyde, polyethylene glycoldiacrylate and formaldehyde is used for the preparation of hydrogels.Chemical modification of allergens for immunotherapy is often achievedby carbamylation with potassium cyanate.

A peptide or variant, wherein the peptide is modified or includesnon-peptide bonds is a preferred embodiment of the invention. Generally,peptides and variants (at least those containing peptide linkagesbetween amino acid residues) may be synthesized by the Fmoc-polyamidemode of solid-phase peptide synthesis as disclosed by Lukas et al.(Lukas et al., 1981) and by references as cited therein. TemporaryN-amino group protection is afforded by the 9-fluorenylmethyloxycarbonyl(Fmoc) group. Repetitive cleavage of this highly base-labile protectinggroup is done using 20% piperidine in N, N-dimethylformamide. Side-chainfunctionalities may be protected as their butyl ethers (in the case ofserine threonine and tyrosine), butyl esters (in the case of glutamicacid and aspartic acid), butyloxycarbonyl derivative (in the case oflysine and histidine), trityl derivative (in the case of cysteine) and4-methoxy-2,3,6-trimethylbenzenesulphonyl derivative (in the case ofarginine). Where glutamine or asparagine are C-terminal residues, use ismade of the 4,4′-dimethoxybenzhydryl group for protection of the sidechain amido functionalities. The solid-phase support is based on apolydimethyl-acrylamide polymer constituted from the three monomersdimethylacrylamide (backbone-monomer), bisacryloylethylene diamine(cross linker) and acryloylsarcosine methyl ester (functionalizingagent). The peptide-to-resin cleavable linked agent used is theacid-labile 4-hydroxymethyl-phenoxyacetic acid derivative. All aminoacid derivatives are added as their preformed symmetrical anhydridederivatives with the exception of asparagine and glutamine, which areadded using a reversed N, N-dicyclohexyl-carbodiimide/1hydroxybenzotriazole mediated coupling procedure. All coupling anddeprotection reactions are monitored using ninhydrin, trinitrobenzenesulphonic acid or isotin test procedures. Upon completion of synthesis,peptides are cleaved from the resin support with concomitant removal ofside-chain protecting groups by treatment with 95% trifluoroacetic acidcontaining a 50% scavenger mix. Scavengers commonly used includeethanedithiol, phenol, anisole and water, the exact choice depending onthe constituent amino acids of the peptide being synthesized. Also acombination of solid phase and solution phase methodologies for thesynthesis of peptides is possible (see, for example, (Bruckdorfer etal., 2004), and the references as cited therein).

Trifluoroacetic acid is removed by evaporation in vacuo, with subsequenttrituration with diethyl ether affording the crude peptide. Anyscavengers present are removed by a simple extraction procedure which onlyophilization of the aqueous phase affords the crude peptide free ofscavengers. Reagents for peptide synthesis are generally available frome.g. Calbiochem-Novabiochem (Nottingham, UK).

Purification may be performed by any one, or a combination of,techniques such as recrystallization, size exclusion chromatography,ion-exchange chromatography, hydrophobic interaction chromatography and(usually) reverse-phase high performance liquid chromatography usinge.g. acetonitril/water gradient separation.

Analysis of peptides may be carried out using thin layer chromatography,electrophoresis, in particular capillary electrophoresis, solid phaseextraction (CSPE), reverse-phase high performance liquid chromatography,amino-acid analysis after acid hydrolysis and by fast atom bombardment(FAB) mass spectrometric analysis, as well as MALDI and ESI-Q-TOF massspectrometric analysis.

In order to select over-presented peptides, a presentation profile iscalculated showing the median sample presentation as well as replicatevariation. The profile juxtaposes samples of the tumor entity ofinterest to a baseline of normal tissue samples. Each of these profilescan then be consolidated into an over-presentation score by calculatingthe p-value of a Linear Mixed-Effects Model (Pinheiro et al., 2015)adjusting for multiple testing by False Discovery Rate (Benjamini andHochberg, 1995) (cf. Example 1).

For the identification and relative quantitation of HLA ligands by massspectrometry, HLA molecules from shock-frozen tissue samples werepurified and HLA-associated peptides were isolated. As peptides derivedfrom prostate-specific antigens can be identified in any prostatetissue, regardless of its benign or malignant state, in addition toprostate cancer tissue specimens also benign prostate hyperplasiasamples were analyzed with the goal to identify peptides encoded byprostate-specific antigens. The isolated peptides were separated andsequences were identified by online nano-electrospray-ionization(nanoESI) liquid chromatography-mass spectrometry (LC-MS) experiments.The resulting peptide sequences were verified by comparison of thefragmentation pattern of natural TUMAPs recorded from prostate cancersamples (N=34 A*02-positive samples and N=37 A*24-positive samples) aswell as additional benign prostatic hyperplasia (N=10 A*02-positivesamples and N=3 A*24-positive samples) with the fragmentation patternsof corresponding synthetic reference peptides of identical sequences.Since the peptides were directly identified as ligands of HLA moleculesof tumorous tissue, these results provide direct evidence for thenatural processing and presentation of the identified peptides ontumorous tissue obtained from 70 patients with a prostate tumor.

The discovery pipeline XPRESIDENT® v2.1 (see, for example, US2013-0096016, which is hereby incorporated by reference in its entirety)allows the identification and selection of relevant over-presentedpeptide vaccine candidates based on direct relative quantitation ofHLA-restricted peptide levels on cancer tissues in comparison to severaldifferent non-cancerous tissues and organs. This was achieved by thedevelopment of label-free differential quantitation using the acquiredLC-MS data processed by a proprietary data analysis pipeline, combiningalgorithms for sequence identification, spectral clustering, ioncounting, retention time alignment, charge state deconvolution andnormalization.

Presentation levels including error estimates for each peptide andsample were established. Peptides exclusively presented on tumor tissueand peptides over-presented in tumor versus non-cancerous tissues andorgans have been identified.

HLA-peptide complexes from prostate tumor tissue samples were purifiedand HLA-associated peptides were isolated and analyzed by LC-MS (seeexamples). All TUMAPs contained in the present application wereidentified with this approach on prostate tumor samples confirming theirpresentation on prostate tumors.

TUMAPs identified on multiple prostate cancer, prostatic hyperplasia andnormal tissues were quantified using ion-counting of label-free LC-MSdata. The method assumes that LC-MS signal areas of a peptide correlatewith its abundance in the sample. All quantitative signals of a peptidein various LC-MS experiments were normalized based on central tendency,averaged per sample and merged into a bar plot, called presentationprofile. The presentation profile consolidates different analysismethods like protein database search, spectral clustering, charge statedeconvolution (decharging) and retention time alignment andnormalization.

Furthermore, the discovery pipeline XPRESIDENT® v2.x allows the directabsolute quantitation of MHC-, preferably HLA-restricted, peptide levelson cancer or other infected tissues. Briefly, the total cell count wascalculated from the total DNA content of the analyzed tissue sample. Thetotal peptide amount for a TUMAP in a tissue sample was measured bynanoLC-MS/MS as the ratio of the natural TUMAP and a known amount of anisotope-labelled version of the TUMAP, the so-called internal standard.The efficiency of TUMAP isolation was determined by spiking peptide:MHCcomplexes of all selected TUMAPs into the tissue lysate at the earliestpossible point of the TUMAP isolation procedure and their detection bynanoLC-MS/MS following completion of the peptide isolation procedure.The total cell count and the amount of total peptide were calculatedfrom triplicate measurements per tissue sample. The peptide-specificisolation efficiencies were calculated as an average from 10 spikeexperiments each measured as a triplicate (see Example 6).

The present invention provides peptides that are useful in treatingcancers/tumors, preferably prostate cancer that over- or exclusivelypresent the peptides of the invention. These peptides were shown by massspectrometry to be naturally presented by HLA molecules on humanprostate tumor samples.

Many of the source gene/proteins (also designated “full-length proteins”or “underlying proteins”) from which the peptides are derived were shownto be highly over-expressed in tumor compared with normaltissues—“normal tissues” in relation to this invention shall meannormal, non-prostatic, tissue cells, demonstrating a high degree oftumor association of the source genes (see Example 2). Moreover, thepeptides themselves are strongly over-presented on tumor tissue—“tumortissue” in relation to this invention shall mean a sample from a patientsuffering from a prostate tumor, but not on normal tissues (see Example1).

HLA-bound peptides can be recognized by the immune system, specificallyT lymphocytes. T cells can destroy the cells presenting the recognizedHLA/peptide complex, e.g. prostate tumor cells presenting the derivedpeptides.

The peptides of the present invention have been shown to be capable ofstimulating T cell responses and/or are over-presented and thus can beused for the production of antibodies and/or TCRs, such as soluble TCRs,according to the present invention (see Example 3, Example 4).Furthermore, the peptides when complexed with the respective MHC can beused for the production of antibodies and/or TCRs, in particular sTCRs,according to the present invention, as well. Respective methods are wellknown to the person of skill, and can be found in the respectiveliterature as well. Thus, the peptides of the present invention areuseful for generating an immune response in a patient by which tumorcells can be destroyed. An immune response in a patient can be inducedby direct administration of the described peptides or suitable precursorsubstances (e.g. elongated peptides, proteins, or nucleic acids encodingthese peptides) to the patient, ideally in combination with an agentenhancing the immunogenicity (i.e. an adjuvant). The immune responseoriginating from such a therapeutic vaccination can be expected to behighly specific against tumor cells because the target peptides of thepresent invention are not presented on normal, non-prostatic, tissues incomparable copy numbers, preventing the risk of undesired autoimmunereactions against normal cells in the patient. Prostate-specificantigens may be a good choice for cancer immunotherapy of prostatecancer because prostate-specific antigens represent tumor-specifictargets in a prostatectomized patient. In a prostate cancer patientwithout prostatectomy, such antigens may also be interesting becauseprostate is not regarded as a vital organ.

The present description further relates to T-cell receptors (TCRs)comprising an alpha chain and a beta chain (“alpha/beta TCRs”). Alsoprovided are inventive peptides capable of binding to TCRs andantibodies when presented by an MHC molecule. The present descriptionalso relates to nucleic acids, vectors and host cells for expressingTCRs and peptides of the present description; and methods of using thesame.

The term “T-cell receptor” (abbreviated TCR) refers to a heterodimericmolecule comprising an alpha polypeptide chain (alpha chain) and a betapolypeptide chain (beta chain), wherein the heterodimeric receptor iscapable of binding to a peptide antigen presented by an HLA molecule.The term also includes so-called gamma/delta TCRs.

In one embodiment the description provides a method of producing a TCRas described herein, the method comprising culturing a host cell capableof expressing the TCR under conditions suitable to promote expression ofthe TCR.

The description in another aspect relates to methods according to thedescription, wherein the antigen is loaded onto class I or II MHCmolecules expressed on the surface of a suitable antigen-presenting cellor artificial antigen-presenting cell by contacting a sufficient amountof the antigen with an antigen-presenting cell or the antigen is loadedonto class I or II MHC tetramers by tetramerizing the antigen/class I orII MHC complex monomers.

The alpha and beta chains of alpha/beta TCR's, and the gamma and deltachains of gamma/delta TCRs, are generally regarded as each having two“domains”, namely variable and constant domains. The variable domainconsists of a concatenation of variable region (V), and joining region(J). The variable domain may also include a leader region (L). Beta anddelta chains may also include a diversity region (D). The alpha and betaconstant domains may also include C-terminal transmembrane (TM) domainsthat anchor the alpha and beta chains to the cell membrane.

With respect to gamma/delta TCRs, the term “TCR gamma variable domain”as used herein refers to the concatenation of the TCR gamma V (TRGV)region without leader region (L), and the TCR gamma J (TRGJ) region, andthe term TCR gamma constant domain refers to the extracellular TRGCregion, or to a C-terminal truncated TRGC sequence. Likewise the term“TCR delta variable domain” refers to the concatenation of the TCR deltaV (TRDV) region without leader region (L) and the TCR delta D/J(TRDD/TRDJ) region, and the term “TCR delta constant domain” refers tothe extracellular TRDC region, or to a C-terminal truncated TRDCsequence.

TCRs of the present description preferably bind to an inventivepeptide-HLA molecule complex with a binding affinity (KD) of about 100μM or less, about 50 μM or less, about 25 μM or less, or about 10 μM orless. More preferred are high affinity TCRs having binding affinities ofabout 1 μM or less, about 100 nM or less, about 50 nM or less, about 25nM or less. Non-limiting examples of preferred binding affinity rangesfor TCRs of the present invention include about 1 nM to about 10 nM;about 10 nM to about 20 nM; about 20 nM to about 30 nM; about 30 nM toabout 40 nM; about 40 nM to about 50 nM; about 50 nM to about 60 nM;about 60 nM to about 70 nM; about 70 nM to about 80 nM; about 80 nM toabout 90 nM; and about 90 nM to about 100 nM.

As used herein in connect with TCRs of the present description,“specific binding” and grammatical variants thereof are used to mean aTCR having a binding affinity (KD) for an inventive peptide-HLA moleculecomplex of 100 μM or less.

Alpha/beta heterodimeric TCRs of the present description may have anintroduced disulfide bond between their constant domains. Preferred TCRsof this type include those which have a TRAC constant domain sequenceand a TRBC1 or TRBC2 constant domain sequence except that Thr 48 of TRACand Ser 57 of TRBC1 or TRBC2 are replaced by cysteine residues, the saidcysteines forming a disulfide bond between the TRAC constant domainsequence and the TRBC1 or TRBC2 constant domain sequence of the TCR.

With or without the introduced inter-chain bond mentioned above,alpha/beta heterodimeric TCRs of the present description may have a TRACconstant domain sequence and a TRBC1 or TRBC2 constant domain sequence,and the TRAC constant domain sequence and the TRBC1 or TRBC2 constantdomain sequence of the TCR may be linked by the native disulfide bondbetween Cys4 of exon 2 of TRAC and Cys2 of exon 2 of TRBC1 or TRBC2.

TCRs of the present description may comprise a detectable label selectedfrom the group consisting of a radionuclide, a fluorophore and biotin.TCRs of the present description may be conjugated to a therapeuticallyactive agent, such as a radionuclide, a chemotherapeutic agent, or atoxin.

In an embodiment, a TCR of the present description having at least onemutation in the alpha chain and/or having at least one mutation in thebeta chain has modified glycosylation compared to the non-mutated TCR.

In an embodiment, a TCR comprising at least one mutation in the TCRalpha chain and/or TCR beta chain has a binding affinity for, and/or abinding half-life for, an inventive peptide-HLA molecule complex, whichis at least double that of a TCR comprising the non-mutated TCR alphachain and/or non-mutated TCR beta chain. Affinity-enhancement oftumor-specific TCRs, and its exploitation, relies on the existence of awindow for optimal TCR affinities. The existence of such a window isbased on observations that TCRs specific for HLA-A2-restricted pathogenshave KD values that are generally about 10-fold lower when compared toTCRs specific for HLA-A2-restricted tumor-associated self-antigens. Itis now known, although tumor antigens have the potential to beimmunogenic, because tumors arise from the individual's own cells onlymutated proteins or proteins with altered translational processing willbe seen as foreign by the immune system. Antigens that are upregulatedor overexpressed (so called self-antigens) will not necessarily induce afunctional immune response against the tumor: T-cells expressing TCRsthat are highly reactive to these antigens will have been negativelyselected within the thymus in a process known as central tolerance,meaning that only T-cells with low-affinity TCRs for self-antigensremain. Therefore, affinity of TCRs or variants of the presentdescription to peptides of the invention can be enhanced by methods wellknown in the art.

The present description further relates to a method of identifying andisolating a TCR according to the present description, said methodcomprising incubating PBMCs from HLA-A*02-negative healthy donors withA2/inventive peptide monomers, incubating the PBMCs withtetramer-phycoerythrin (PE) and isolating the high avidity T-cells byfluorescence activated cell sorting (FACS)—Calibur analysis.

The present description further relates to a method of identifying andisolating a TCR according to the present description, said methodcomprising obtaining a transgenic mouse with the entire human TCRαβ geneloci (1.1 and 0.7 Mb), whose T-cells express a diverse human TCRrepertoire that compensates for mouse TCR deficiency, immunizing themouse with HAVCR1-001, incubating PBMCs obtained from the transgenicmice with tetramer-phycoerythrin (PE), and isolating the high avidityT-cells by fluorescence activated cell sorting (FACS)—Calibur analysis.

In one aspect, to obtain T-cells expressing TCRs of the presentdescription, nucleic acids encoding TCR-alpha and/or TCR-beta chains ofthe present description are cloned into expression vectors, such asgamma retrovirus or lentivirus. The recombinant viruses are generatedand then tested for functionality, such as antigen specificity andfunctional avidity. An aliquot of the final product is then used totransduce the target T-cell population (generally purified from patientPBMCs), which is expanded before infusion into the patient.

In another aspect, to obtain T-cells expressing TCRs of the presentdescription, TCR RNAs are synthesized by techniques known in the art,e.g., in vitro transcription systems. The in vitro-synthesized TCR RNAsare then introduced into primary CD8+ T-cells obtained from healthydonors by electroporation to re-express tumor specific TCR-alpha and/orTCR-beta chains.

To increase the expression, nucleic acids encoding TCRs of the presentdescription may be operably linked to strong promoters, such asretroviral long terminal repeats (LTRs), cytomegalovirus (CMV), murinestem cell virus (MSCV) U3, phosphoglycerate kinase (PGK), β-actin,ubiquitin, and a simian virus 40 (SV40)/CD43 composite promoter,elongation factor (EF)-1a and the spleen focus-forming virus (SFFV)promoter.

In a preferred embodiment, the promoter is heterologous to the nucleicacid being expressed.

In addition to strong promoters, TCR expression cassettes of the presentdescription may contain additional elements that can enhance transgeneexpression, including a central polypurine tract (cPPT), which promotesthe nuclear translocation of lentiviral constructs (Follenzi et al.,2000), and the woodchuck hepatitis virus posttranscriptional regulatoryelement (wPRE), which increases the level of transgene expression byincreasing RNA stability (Zufferey et al., 1999).

The alpha and beta chains of a TCR of the present invention may beencoded by nucleic acids located in separate vectors, or may be encodedby polynucleotides located in the same vector.

Achieving high-level TCR surface expression requires that both theTCR-alpha and TCR-beta chains of the introduced TCR be transcribed athigh levels. To do so, the TCR-alpha and TCR-beta chains of the presentdescription may be cloned into bicistronic constructs in a singlevector, which has been shown to be capable of overcoming this obstacle.The use of a viral intra-ribosomal entry site (IRES) between theTCR-alpha and TCR-beta chains results in the coordinated expression ofboth chains, because the TCR-alpha and TCR-beta chains are generatedfrom a single transcript that is broken into two proteins duringtranslation, ensuring that an equal molar ratio of TCR-alpha andTCR-beta chains are produced. (Schmitt et al. 2009).

Nucleic acids encoding TCRs of the present description may be codonoptimized to increase expression from a host cell. Redundancy in thegenetic code allows some amino acids to be encoded by more than onecodon, but certain codons are less “optimal” than others because of therelative availability of matching tRNAs as well as other factors(Gustafsson et al., 2004). Modifying the TCR-alpha and TCR-beta genesequences such that each amino acid is encoded by the optimal codon formammalian gene expression, as well as eliminating mRNA instabilitymotifs or cryptic splice sites, has been shown to significantly enhanceTCR-alpha and TCR-beta gene expression (Scholten et al., 2006).

Furthermore, mispairing between the introduced and endogenous TCR chainsmay result in the acquisition of specificities that pose a significantrisk for autoimmunity. For example, the formation of mixed TCR dimersmay reduce the number of CD3 molecules available to form properly pairedTCR complexes, and therefore can significantly decrease the functionalavidity of the cells expressing the introduced TCR (Kuball et al.,2007).

To reduce mispairing, the C-terminus domain of the introduced TCR chainsof the present description may be modified in order to promoteinterchain affinity, while de-creasing the ability of the introducedchains to pair with the endogenous TCR. These strategies may includereplacing the human TCR-alpha and TCR-beta C-terminus domains with theirmurine counterparts (murinized C-terminus domain); generating a secondinterchain disulfide bond in the C-terminus domain by introducing asecond cysteine residue into both the TCR-alpha and TCR-beta chains ofthe introduced TCR (cysteine modification); swapping interactingresidues in the TCR-alpha and TCR-beta chain C-terminus domains(“knob-in-hole”); and fusing the variable domains of the TCR-alpha andTCR-beta chains directly to CD3 (CD3 fusion). (Schmitt et al. 2009).

In an embodiment, a host cell is engineered to express a TCR of thepresent description. In preferred embodiments, the host cell is a humanT-cell or T-cell progenitor. In some embodiments the T-cell or T-cellprogenitor is obtained from a cancer patient. In other embodiments theT-cell or T-cell progenitor is obtained from a healthy donor. Host cellsof the present description can be allogeneic or autologous with respectto a patient to be treated. In one embodiment, the host is a gamma/deltaT-cell transformed to express an alpha/beta TCR.

A “pharmaceutical composition” is a composition suitable foradministration to a human being in a medical setting. Preferably, apharmaceutical composition is sterile and produced according to GMPguidelines.

The pharmaceutical compositions comprise the peptides either in the freeform or in the form of a pharmaceutically acceptable salt (see alsoabove). As used herein, “a pharmaceutically acceptable salt” refers to aderivative of the disclosed peptides wherein the peptide is modified bymaking acid or base salts of the agent. For example, acid salts areprepared from the free base (typically wherein the neutral form of thedrug has a neutral —NH₂ group) involving reaction with a suitable acid.Suitable acids for preparing acid salts include both organic acids,e.g., acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalicacid, malic acid, malonic acid, succinic acid, maleic acid, fumaricacid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelicacid, methane sulfonic acid, ethane sulfonic acid, p-toluenesulfonicacid, salicylic acid, and the like, as well as inorganic acids, e.g.,hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acidphosphoric acid and the like. Conversely, preparation of basic salts ofacid moieties which may be present on a peptide are prepared using apharmaceutically acceptable base such as sodium hydroxide, potassiumhydroxide, ammonium hydroxide, calcium hydroxide, trimethylamine or thelike.

In an especially preferred embodiment, the pharmaceutical compositionscomprise the peptides as salts of acetic acid (acetates), trifluoroacetates or hydrochloric acid (chlorides).

Preferably, the medicament of the present invention is animmunotherapeutic, such as a vaccine. It may be administered directlyinto the patient, into the affected organ or systemically i.d., i.m.,s.c., i.p. and i.v., or applied ex vivo to cells derived from thepatient or a human cell line which are subsequently administered to thepatient, or used in vitro to select a subpopulation of immune cellsderived from the patient, which are then re-administered to the patient.If the nucleic acid is administered to cells in vitro, it may be usefulfor the cells to be transfected so as to co-express immune-stimulatingcytokines, such as interleukin-2. The peptide may be substantially pure,or combined with an immune-stimulating adjuvant (see below) or used incombination with immune-stimulatory cytokines, or be administered with asuitable delivery system, for example liposomes. The peptide may also beconjugated to a suitable carrier such as keyhole limpet haemocyanin(KLH) or mannan (see WO 95/18145 and (Longenecker et al., 1993)). Thepeptide may also be tagged, may be a fusion protein, or may be a hybridmolecule. The peptides whose sequence is given in the present inventionare expected to stimulate CD4 or CD8 T cells. However, stimulation ofCD8 T cells is more efficient in the presence of help provided by CD4T-helper cells. Thus, for MHC Class I epitopes that stimulate CD8 Tcells the fusion partner or sections of a hybrid molecule suitablyprovide epitopes which stimulate CD4-positive T cells. CD4- andCD8-stimulating epitopes are well known in the art and include thoseidentified in the present invention.

In one aspect, the vaccine comprises at least one peptide having theamino acid sequence set forth SEQ ID No. 1 to SEQ ID No. 48, and atleast one additional peptide, preferably two to 50, more preferably twoto 25, even more preferably two to 20 and most preferably two, three,four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen,fourteen, fifteen, sixteen, seventeen or eighteen peptides. Thepeptide(s) may be derived from one or more specific TAAs and may bind toMHC class I molecules.

A further aspect of the invention provides a nucleic acid (for example apolynucleotide) encoding a peptide or peptide variant of the invention.The polynucleotide may be, for example, DNA, cDNA, PNA, RNA orcombinations thereof, either single- and/or double-stranded, or nativeor stabilized forms of polynucleotides, such as, for example,polynucleotides with a phosphorothioate backbone and it may or may notcontain introns so long as it codes for the peptide. Of course, onlypeptides that contain naturally occurring amino acid residues joined bynaturally occurring peptide bonds are encodable by a polynucleotide. Astill further aspect of the invention provides an expression vectorcapable of expressing a polypeptide according to the invention.

A variety of methods have been developed to link polynucleotides,especially DNA, to vectors for example via complementary cohesivetermini. For instance, complementary homopolymer tracts can be added tothe DNA segment to be inserted to the vector DNA. The vector and DNAsegment are then joined by hydrogen bonding between the complementaryhomopolymeric tails to form recombinant DNA molecules.

Synthetic linkers containing one or more restriction sites provide analternative method of joining the DNA segment to vectors. Syntheticlinkers containing a variety of restriction endonuclease sites arecommercially available from a number of sources including InternationalBiotechnologies Inc. New Haven, Conn., USA.

A desirable method of modifying the DNA encoding the polypeptide of theinvention employs the polymerase chain reaction as disclosed by Saiki RK, et al. (Saiki et al., 1988). This method may be used for introducingthe DNA into a suitable vector, for example by engineering in suitablerestriction sites, or it may be used to modify the DNA in other usefulways as is known in the art. If viral vectors are used, pox- oradenovirus vectors are preferred.

The DNA (or in the case of retroviral vectors, RNA) may then beexpressed in a suitable host to produce a polypeptide comprising thepeptide or variant of the invention. Thus, the DNA encoding the peptideor variant of the invention may be used in accordance with knowntechniques, appropriately modified in view of the teachings containedherein, to construct an expression vector, which is then used totransform an appropriate host cell for the expression and production ofthe polypeptide of the invention. Such techniques include thosedisclosed, for example, in U.S. Pat. Nos. 4,440,859, 4,530,901,4,582,800, 4,677,063, 4,678,751, 4,704,362, 4,710,463, 4,757,006,4,766,075, and 4,810,648.

The DNA (or in the case of retroviral vectors, RNA) encoding thepolypeptide constituting the compound of the invention may be joined toa wide variety of other DNA sequences for introduction into anappropriate host. The companion DNA will depend upon the nature of thehost, the manner of the introduction of the DNA into the host, andwhether episomal maintenance or integration is desired.

Generally, the DNA is inserted into an expression vector, such as aplasmid, in proper orientation and correct reading frame for expression.If necessary, the DNA may be linked to the appropriate transcriptionaland translational regulatory control nucleotide sequences recognized bythe desired host, although such controls are generally available in theexpression vector. The vector is then introduced into the host throughstandard techniques. Generally, not all of the hosts will be transformedby the vector. Therefore, it will be necessary to select for transformedhost cells. One selection technique involves incorporating into theexpression vector a DNA sequence, with any necessary control elements,that codes for a selectable trait in the transformed cell, such asantibiotic resistance.

Alternatively, the gene for such selectable trait can be on anothervector, which is used to co-transform the desired host cell.

Host cells that have been transformed by the recombinant DNA of theinvention are then cultured for a sufficient time and under appropriateconditions known to those skilled in the art in view of the teachingsdisclosed herein to permit the expression of the polypeptide, which canthen be recovered.

Many expression systems are known, including bacteria (for example E.coli and Bacillus subtilis), yeasts (for example Saccharomycescerevisiae), filamentous fungi (for example Aspergillus spec.), plantcells, animal cells and insect cells. Preferably, the system can bemammalian cells such as CHO cells available from the ATCC Cell BiologyCollection.

A typical mammalian cell vector plasmid for constitutive expressioncomprises the CMV or SV40 promoter with a suitable poly A tail and aresistance marker, such as neomycin. One example is pSVL available fromPharmacia, Piscataway, N.J., USA. An example of an inducible mammalianexpression vector is pMSG, also available from Pharmacia. Useful yeastplasmid vectors are pRS403-406 and pRS413-416 and are generallyavailable from Stratagene Cloning Systems, La Jolla, Calif. 92037, USA.Plasmids pRS403, pRS404, pRS405 and pRS406 are Yeast Integratingplasmids (YIps) and incorporate the yeast selectable markers HIS3, TRP1,LEU2 and URA3. Plasmids pRS413-416 are Yeast Centromere plasmids (Ycps).CMV promoter-based vectors (for example from Sigma-Aldrich) providetransient or stable expression, cytoplasmic expression or secretion, andN-terminal or C-terminal tagging in various combinations of FLAG,3×FLAG, c-myc or MAT. These fusion proteins allow for detection,purification and analysis of recombinant protein. Dual-tagged fusionsprovide flexibility in detection.

The strong human cytomegalovirus (CMV) promoter regulatory region drivesconstitutive protein expression levels as high as 1 mg/L in COS cells.For less potent cell lines, protein levels are typically ˜0.1 mg/L. Thepresence of the SV40 replication origin will result in high levels ofDNA replication in SV40 replication permissive COS cells. CMV vectors,for example, can contain the pMB1 (derivative of pBR322) origin forreplication in bacterial cells, the b-lactamase gene for ampicillinresistance selection in bacteria, hGH polyA, and the f1 origin. Vectorscontaining the pre-pro-trypsin leader (PPT) sequence can direct thesecretion of FLAG fusion proteins into the culture medium forpurification using ANTI-FLAG antibodies, resins, and plates. Othervectors and expression systems are well known in the art for use with avariety of host cells.

In another embodiment two or more peptides or peptide variants of theinvention are encoded and thus expressed in a successive order (similarto “beads on a string” constructs). In doing so, the peptides or peptidevariants may be linked or fused together by stretches of linker aminoacids, such as for example LLLLLL, or may be linked without anyadditional peptide(s) between them. These constructs can also be usedfor cancer therapy, and may induce immune responses both involving MHC Iand MHC II.

The present invention also relates to a host cell transformed with apolynucleotide vector construct of the present invention. The host cellcan be either prokaryotic or eukaryotic. Bacterial cells may bepreferred prokaryotic host cells in some circumstances and typically area strain of E. coli such as, for example, the E. coli strains DH5available from Bethesda Research Laboratories Inc., Bethesda, Md., USA,and RR1 available from the American Type Culture Collection (ATCC) ofRockville, Md., USA (No ATCC 31343). Preferred eukaryotic host cellsinclude yeast, insect and mammalian cells, preferably vertebrate cellssuch as those from a mouse, rat, monkey or human fibroblastic and coloncell lines. Yeast host cells include YPH499, YPH500 and YPH501, whichare generally available from Stratagene Cloning Systems, La Jolla,Calif. 92037, USA. Preferred mammalian host cells include Chinesehamster ovary (CHO) cells available from the ATCC as CCL61, NIH Swissmouse embryo cells NIH/3T3 available from the ATCC as CRL 1658, monkeykidney-derived COS-1 cells available from the ATCC as CRL 1650 and 293cells which are human embryonic kidney cells. Preferred insect cells areSf9 cells which can be transfected with baculovirus expression vectors.An overview regarding the choice of suitable host cells for expressioncan be found in, for example, the textbook of Paulina Balbás and ArgeliaLorence “Methods in Molecular Biology Recombinant Gene Expression,Reviews and Protocols,” Part One, Second Edition, ISBN978-1-58829-262-9, and other literature known to the person of skill.

Transformation of appropriate cell hosts with a DNA construct of thepresent invention is accomplished by well-known methods that typicallydepend on the type of vector used. With regard to transformation ofprokaryotic host cells, see, for example, Cohen et al. (Cohen et al.,1972) and (Green and Sambrook, 2012). Transformation of yeast cells isdescribed in Sherman et al. (Sherman et al., 1986). The method of Beggs(Beggs, 1978) is also useful. With regard to vertebrate cells, reagentsuseful in transfecting such cells, for example calcium phosphate andDEAE-dextran or liposome formulations, are available from StratageneCloning Systems, or Life Technologies Inc., Gaithersburg, Md. 20877,USA. Electroporation is also useful for transforming and/or transfectingcells and is well known in the art for transforming yeast cell,bacterial cells, insect cells and vertebrate cells.

Successfully transformed cells, i.e. cells that contain a DNA constructof the present invention, can be identified by well-known techniquessuch as PCR. Alternatively, the presence of the protein in thesupernatant can be detected using antibodies.

It will be appreciated that certain host cells of the invention areuseful in the preparation of the peptides of the invention, for examplebacterial, yeast and insect cells. However, other host cells may beuseful in certain therapeutic methods. For example, antigen-presentingcells, such as dendritic cells, may usefully be used to express thepeptides of the invention such that they may be loaded into appropriateMHC molecules. Thus, the current invention provides a host cellcomprising a nucleic acid or an expression vector according to theinvention.

In a preferred embodiment the host cell is an antigen presenting cell,in particular a dendritic cell or antigen presenting cell. APCs loadedwith a recombinant fusion protein containing prostatic acid phosphatase(PAP) were approved by the U.S. Food and Drug Administration (FDA) onApr. 29, 2010, to treat asymptomatic or minimally symptomatic metastaticHRPC (Sipuleucel-T) (Rini et al., 2006; Small et al., 2006).

A further aspect of the invention provides a method of producing apeptide or its variant, the method comprising culturing a host cell andisolating the peptide from the host cell or its culture medium.

In another embodiment the peptide, the nucleic acid or the expressionvector of the invention are used in medicine. For example, the peptideor its variant may be prepared for intravenous (i.v.) injection,sub-cutaneous (s.c.) injection, intradermal (i.d.) injection,intraperitoneal (i.p.) injection, intramuscular (i.m.) injection.Preferred methods of peptide injection include s.c., i.d., i.p., i.m.,and i.v. Preferred methods of DNA injection include i.d., i.m., s.c.,i.p. and i.v. Doses of e.g. between 50 μg and 1.5 mg, preferably 125 μgto 500 μg, of peptide or DNA may be given and will depend on therespective peptide or DNA. Dosages of this range were successfully usedin previous trials (Walter et al., 2012).

The polynucleotide used for active vaccination may be substantiallypure, or contained in a suitable vector or delivery system. The nucleicacid may be DNA, cDNA, PNA, RNA or a combination thereof. Methods fordesigning and introducing such a nucleic acid are well known in the art.An overview is provided by e.g. Teufel et al. (Teufel et al., 2005).Polynucleotide vaccines are easy to prepare, but the mode of action ofthese vectors in inducing an immune response is not fully understood.Suitable vectors and delivery systems include viral DNA and/or RNA, suchas systems based on adenovirus, vaccinia virus, retroviruses, herpesvirus, adeno-associated virus or hybrids containing elements of morethan one virus. Non-viral delivery systems include cationic lipids andcationic polymers and are well known in the art of DNA delivery.Physical delivery, such as via a “gene-gun” may also be used. Thepeptide or peptides encoded by the nucleic acid may be a fusion protein,for example with an epitope that stimulates T cells for the respectiveopposite CDR as noted above.

The medicament of the invention may also include one or more adjuvants.Adjuvants are substances that non-specifically enhance or potentiate theimmune response (e.g., immune responses mediated by CD8-positive T cellsand helper-T (TH) cells to an antigen, and would thus be considereduseful in the medicament of the present invention. Suitable adjuvantsinclude, but are not limited to, 1018 ISS, aluminum salts, AMPLIVAX®,AS15, BCG, CP-870,893, CpG7909, CyaA, dSLIM, flagellin or TLR5 ligandsderived from flagellin, FLT3 ligand, GM-CSF, IC30, IC31, Imiquimod(ALDARA®), resiquimod, ImuFact IMP321, Interleukins as IL-2, IL-13,IL-21, Interferon-alpha or -beta, or pegylated derivatives thereof, ISPatch, ISS, ISCOMATRIX, ISCOMs, JuvImmune®, LipoVac, MALP2, MF59,monophosphoryl lipid A, Montanide IMS 1312, Montanide ISA 206, MontanideISA 50V, Montanide ISA-51, water-in-oil and oil-in-water emulsions,OK-432, OM-174, OM-197-MP-EC, ONTAK, OspA, PepTel® vector system,poly(lactid co-glycolid) [PLG]-based and dextran microparticles,talactoferrin SRL172, Virosomes and other Virus-like particles, YF-17D,VEGF trap, R848, beta-glucan, Pam3Cys, Aquila's QS21 stimulon, which isderived from saponin, mycobacterial extracts and synthetic bacterialcell wall mimics, and other proprietary adjuvants such as Ribi's Detox,Quil, or Superfos. Adjuvants such as Freund's or GM-CSF are preferred.Several immunological adjuvants (e.g., MF59) specific for dendriticcells and their preparation have been described previously (Allison andKrummel, 1995). Also cytokines may be used. Several cytokines have beendirectly linked to influencing dendritic cell migration to lymphoidtissues (e.g., TNF-), accelerating the maturation of dendritic cellsinto efficient antigen-presenting cells for T-lymphocytes (e.g., GM-CSF,IL-1 and IL-4) (U.S. Pat. No. 5,849,589, specifically incorporatedherein by reference in its entirety) and acting as immunoadjuvants(e.g., IL-12, IL-15, IL-23, IL-7, IFN-alpha. IFN-beta) (Gabrilovich etal., 1996).

CpG immunostimulatory oligonucleotides have also been reported toenhance the effects of adjuvants in a vaccine setting. Without beingbound by theory, CpG oligonucleotides act by activating the innate(non-adaptive) immune system via Toll-like receptors (TLR), mainly TLR9.CpG triggered TLR9 activation enhances antigen-specific humoral andcellular responses to a wide variety of antigens, including peptide orprotein antigens, live or killed viruses, dendritic cell vaccines,autologous cellular vaccines and polysaccharide conjugates in bothprophylactic and therapeutic vaccines. More importantly it enhancesdendritic cell maturation and differentiation, resulting in enhancedactivation of TH1 cells and strong cytotoxic T-lymphocyte (CTL)generation, even in the absence of CD4 T cell help. The TH1 bias inducedby TLR9 stimulation is maintained even in the presence of vaccineadjuvants such as alum or incomplete Freund's adjuvant (IFA) thatnormally promote a TH2 bias. CpG oligonucleotides show even greateradjuvant activity when formulated or co-administered with otheradjuvants or in formulations such as microparticles, nanoparticles,lipid emulsions or similar formulations, which are especially necessaryfor inducing a strong response when the antigen is relatively weak. Theyalso accelerate the immune response and enable the antigen doses to bereduced by approximately two orders of magnitude, with comparableantibody responses to the full-dose vaccine without CpG in someexperiments (Krieg, 2006). U.S. Pat. No. 6,406,705 B1 describes thecombined use of CpG oligonucleotides, non-nucleic acid adjuvants and anantigen to induce an antigen-specific immune response. A CpG TLR9antagonist is dSLIM (double Stem Loop Immunomodulator) by Mologen(Berlin, Germany) which is a preferred component of the pharmaceuticalcomposition of the present invention. Other TLR binding molecules suchas RNA binding TLR 7, TLR 8 and/or TLR 9 may also be used.

Other examples for useful adjuvants include, but are not limited tochemically modified CpGs (e.g. CpR, Idera), dsRNA analogues such asPoly(I:C) and derivatives thereof (e.g. AmpliGen®, Hiltonol®,poly-(ICLC), poly(IC-R), poly(I:C12U), non-CpG bacterial DNA or RNA aswell as immunoactive small molecules and antibodies such ascyclophosphamide, sunitinib, Bevacizumab®, celebrex, NCX-4016,sildenafil, tadalafil, vardenafil, sorafenib, temozolomide,temsirolimus, XL-999, CP-547632, pazopanib, VEGF Trap, ZD2171, AZD2171,anti-CTLA4, other antibodies targeting key structures of the immunesystem (e.g. anti-CD40, anti-TGFbeta, anti-TNFalpha receptor) andSC58175, which may act therapeutically and/or as an adjuvant. Theamounts and concentrations of adjuvants and additives useful in thecontext of the present invention can readily be determined by theskilled artisan without undue experimentation.

Preferred adjuvants are anti-CD40, imiquimod, resiquimod, GM-CSF,cyclophosphamide, sunitinib, bevacizumab, interferon-alpha, CpGoligonucleotides and derivates, poly-(I:C) and derivates, RNA,sildenafil, and particulate formulations with PLG or virosomes.

In a preferred embodiment, the pharmaceutical composition according tothe invention the adjuvant is selected from the group consisting ofcolony-stimulating factors, such as Granulocyte Macrophage ColonyStimulating Factor (GM-CSF, sargramostim), cyclophosphamide, imiquimod,resiquimod, and interferon-alpha.

In a preferred embodiment, the pharmaceutical composition according tothe invention the adjuvant is selected from the group consisting ofcolony-stimulating factors, such as Granulocyte Macrophage ColonyStimulating Factor (GM-CSF, sargramostim), cyclophosphamide, imiquimodand resiquimod. In a preferred embodiment of the pharmaceuticalcomposition according to the invention, the adjuvant iscyclophosphamide, imiquimod or resiquimod. Even more preferred adjuvantsare Montanide IMS 1312, Montanide ISA 206, Montanide ISA 50V, MontanideISA-51, poly-ICLC (Hiltonol®) and anti-CD40 mAB, or combinationsthereof.

This composition is used for parenteral administration, such assubcutaneous, intradermal, intramuscular or oral administration. Forthis, the peptides and optionally other molecules are dissolved orsuspended in a pharmaceutically acceptable, preferably aqueous carrier.In addition, the composition can contain excipients, such as buffers,binding agents, blasting agents, diluents, flavors, lubricants, etc. Thepeptides can also be administered together with immune stimulatingsubstances, such as cytokines. An extensive listing of excipients thatcan be used in such a composition, can be, for example, taken from A.Kibbe, Handbook of Pharmaceutical Excipients (Kibbe, 2000). Thecomposition can be used for a prevention, prophylaxis and/or therapy ofadenomateous or cancerous diseases. Exemplary formulations can be foundin, for example, EP2112253.

It is important to realize that the immune response triggered by thevaccine according to the invention attacks the cancer in differentcell-stages and different stages of development. Furthermore differentcancer associated signaling pathways are attacked. This is an advantageover vaccines that address only one or few targets, which may cause thetumor to easily adapt to the attack (tumor escape). Furthermore, not allindividual tumors express the same pattern of antigens. Therefore, acombination of several tumor-associated peptides ensures that everysingle tumor bears at least some of the targets. The composition isdesigned in such a way that each tumor is expected to express several ofthe antigens and cover several independent pathways necessary for tumorgrowth and maintenance. Thus, the vaccine can easily be used“off-the-shelf” for a larger patient population. This means that apre-selection of patients to be treated with the vaccine can berestricted to HLA typing, does not require any additional biomarkerassessments for antigen expression, but it is still ensured that severaltargets are simultaneously attacked by the induced immune response,which is important for efficacy (Banchereau et al., 2001; Walter et al.,2012).

As used herein, the term “scaffold” refers to a molecule thatspecifically binds to an (e.g. antigenic) determinant. In oneembodiment, a scaffold is able to direct the entity to which it isattached (e.g. a (second) antigen binding moiety) to a target site, forexample to a specific type of tumor cell or tumor stroma bearing theantigenic determinant (e.g. the complex of a peptide with MHC, accordingto the application at hand). In another embodiment a scaffold is able toactivate signaling through its target antigen, for example a T cellreceptor complex antigen. Scaffolds include but are not limited toantibodies and fragments thereof, antigen binding domains of anantibody, comprising an antibody heavy chain variable region and anantibody light chain variable region, binding proteins comprising atleast one ankyrin repeat motif and single domain antigen binding (SDAB)molecules, aptamers, (soluble) TCRs and (modified) cells such asallogenic or autologous T cells. To assess whether a molecule is ascaffold binding to a target, binding assays can be performed.

“Specific” binding means that the scaffold binds the peptide-MHC-complexof interest better than other naturally occurring peptide-MHC-complexes,to an extent that a scaffold armed with an active molecule that is ableto kill a cell bearing the specific target is not able to kill anothercell without the specific target but presenting other peptide-MHCcomplex(es). Binding to other peptide-MHC complexes is irrelevant if thepeptide of the cross-reactive peptide-MHC is not naturally occurring,i.e. not derived from the human HLA-peptidome. Tests to assess targetcell killing are well known in the art. They should be performed usingtarget cells (primary cells or cell lines) with unaltered peptide-MHCpresentation, or cells loaded with peptides such that naturallyoccurring peptide-MHC levels are reached.

Each scaffold can comprise a labelling which provides that the boundscaffold can be detected by determining the presence or absence of asignal provided by the label. For example, the scaffold can be labelledwith a fluorescent dye or any other applicable cellular marker molecule.Such marker molecules are well known in the art. For example afluorescence-labelling, for example provided by a fluorescence dye, canprovide a visualization of the bound aptamer by fluorescence or laserscanning microscopy or flow cytometry.

Each scaffold can be conjugated with a second active molecule such asfor example IL-21, anti-CD3, anti-CD28.

For further information on polypeptide scaffolds see for example thebackground section of WO 2014/071978A1 and the references cited therein.

The present invention further relates to aptamers. Aptamers (see forexample WO 2014/191359 and the literature as cited therein) are shortsingle-stranded nucleic acid molecules, which can fold into definedthree-dimensional structures and recognize specific target structures.They have appeared to be suitable alternatives for developing targetedtherapies. Aptamers have been shown to selectively bind to a variety ofcomplex targets with high affinity and specificity.

Aptamers recognizing cell surface located molecules have been identifiedwithin the past decade and provide means for developing diagnostic andtherapeutic approaches. Since aptamers have been shown to possess almostno toxicity and immunogenicity they are promising candidates forbiomedical applications. Indeed aptamers, for example prostate-specificmembrane-antigen recognizing aptamers, have been successfully employedfor targeted therapies and shown to be functional in xenograft in vivomodels. Furthermore, aptamers recognizing specific tumor cell lines havebeen identified.

DNA aptamers can be selected to reveal broad-spectrum recognitionproperties for various cancer cells, and particularly those derived fromsolid tumors, while non-tumorigenic and primary healthy cells are notrecognized. If the identified aptamers recognize not only a specifictumor sub-type but rather interact with a series of tumors, this rendersthe aptamers applicable as so-called broad-spectrum diagnostics andtherapeutics.

Further, investigation of cell-binding behavior with flow cytometryshowed that the aptamers revealed very good apparent affinities that arewithin the nanomolar range.

Aptamers are useful for diagnostic and therapeutic purposes. Further, itcould be shown that some of the aptamers are taken up by tumor cells andthus can function as molecular vehicles for the targeted delivery ofanti-cancer agents such as siRNA into tumor cells.

Aptamers can be selected against complex targets such as cells andtissues and complexes of the peptides comprising, preferably consistingof, a sequence according to any of SEQ ID No 1 to SEQ ID No 48,according to the invention at hand with the MHC molecule, using thecell-SELEX (Systematic Evolution of Ligands by Exponential enrichment)technique.

The peptides of the present invention can be used to generate anddevelop specific antibodies against MHC/peptide complexes. These can beused for therapy, targeting toxins or radioactive substances to thediseased tissue. Another use of these antibodies can be targetingradionuclides to the diseased tissue for imaging purposes such as PET.This use can help to detect small metastases or to determine the sizeand precise localization of diseased tissues.

Therefore, it is a further aspect of the invention to provide a methodfor producing a recombinant antibody specifically binding to a humanmajor histocompatibility complex (MHC) class I or II being complexedwith a HLA-restricted antigen, the method comprising: immunizing agenetically engineered non-human mammal comprising cells expressing saidhuman major histocompatibility complex (MHC) class I or II with asoluble form of a MHC class I or II molecule being complexed with saidHLA-restricted antigen; isolating mRNA molecules from antibody producingcells of said non-human mammal; producing a phage display librarydisplaying protein molecules encoded by said mRNA molecules; andisolating at least one phage from said phage display library, said atleast one phage displaying said antibody specifically binding to saidhuman major histocompatibility complex (MHC) class I or II beingcomplexed with said HLA-restricted antigen.

It is a further aspect of the invention to provide an antibody thatspecifically binds to a human major histocompatibility complex (MHC)class I or II being complexed with a HLA-restricted antigen, wherein theantibody preferably is a polyclonal antibody, monoclonal antibody,bi-specific antibody and/or a chimeric antibody.

Respective methods for producing such antibodies and single chain classI major histocompatibility complexes, as well as other tools for theproduction of these antibodies are disclosed in WO 03/068201, WO2004/084798, WO 01/72768, WO 03/070752, and in publications (Cohen etal., 2003a; Cohen et al., 2003b; Denkberg et al., 2003), which for thepurposes of the present invention are all explicitly incorporated byreference in their entireties.

Preferably, the antibody is binding with a binding affinity of below 20nanomolar, preferably of below 10 nanomolar, to the complex, which isalso regarded as “specific” in the context of the present invention.

The present invention relates to a peptide comprising a sequence that isselected from the group consisting of SEQ ID No: 1 to SEQ ID No: 48, ora variant thereof which is at least 88% homologous (preferablyidentical) to SEQ ID No: 1 to SEQ ID No: 48 or a variant thereof thatinduces T cells cross-reacting with said peptide, wherein said peptideis not the underlying full-length polypeptide.

The present invention further relates to a peptide comprising a sequencethat is selected from the group consisting of SEQ ID No: 1 to SEQ ID No:48 or a variant thereof which is at least 88% homologous (preferablyidentical) to SEQ ID No: 1 to SEQ ID No: 48, wherein said peptide orvariant has an overall length of between 8 and 100, preferably between 8and 30, and most preferred between 8 and 14 amino acids.

The present invention further relates to the peptides according to theinvention that have the ability to bind to a molecule of the human majorhistocompatibility complex (MHC) class-I or -II.

The present invention further relates to the peptides according to theinvention wherein the peptide consists or consists essentially of anamino acid sequence according to SEQ ID No: 1 to SEQ ID No: 48.

The present invention further relates to the peptides according to theinvention, wherein the peptide is (chemically) modified and/or includesnon-peptide bonds.

The present invention further relates to the peptides according to theinvention, wherein the peptide is part of a fusion protein, inparticular comprising N-terminal amino acids of the HLA-DRantigen-associated invariant chain (Ii), or wherein the peptide is fusedto (or into) an antibody, such as, for example, an antibody that isspecific for dendritic cells.

The present invention further relates to a nucleic acid, encoding thepeptides according to the invention, provided that the peptide is notthe complete (full) human protein.

The present invention further relates to the nucleic acid according tothe invention that is DNA, cDNA, PNA, RNA or combinations thereof.

The present invention further relates to an expression vector capable ofexpressing a nucleic acid according to the present invention.

The present invention further relates to a peptide according to thepresent invention, a nucleic acid according to the present invention oran expression vector according to the present invention for use inmedicine, in particular in the treatment of prostate cancer.

The present invention further relates to a host cell comprising anucleic acid according to the invention or an expression vectoraccording to the invention.

The present invention further relates to the host cell according to thepresent invention that is an antigen presenting cell, and preferably adendritic cell.

The present invention further relates to a method of producing a peptideaccording to the present invention, said method comprising culturing thehost cell according to the present invention, and isolating the peptidefrom said host cell or its culture medium.

The present invention further relates to the method according to thepresent invention, where-in the antigen is loaded onto class I or II MHCmolecules expressed on the surface of a suitable antigen-presenting cellby contacting a sufficient amount of the antigen with anantigen-presenting cell.

The present invention further relates to the method according to theinvention, wherein the antigen-presenting cell comprises an expressionvector capable of expressing said peptide containing SEQ ID No: 1 to SEQID No: 48 or said variant amino acid sequence.

The present invention further relates to activated T cells, produced bythe method according to the present invention, wherein said T cellsselectively recognizes a cell which aberrantly expresses a polypeptidecomprising an amino acid sequence according to the present invention.

The present invention further relates to a method of killing targetcells in a patient which target cells aberrantly express a polypeptidecomprising any amino acid sequence according to the present invention,the method comprising administering to the patient an effective numberof T cells as according to the present invention.

The present invention further relates to the use of any peptidedescribed, a nucleic acid according to the present invention, anexpression vector according to the present invention, a cell accordingto the present invention, or an activated cytotoxic T lymphocyteaccording to the present invention as a medicament or in the manufactureof a medicament. The present invention further relates to a useaccording to the present invention, wherein the medicament is activeagainst cancer.

The present invention further relates to a use according to theinvention, wherein the medicament is a vaccine. The present inventionfurther relates to a use according to the invention, wherein themedicament is active against cancer.

The present invention further relates to a use according to theinvention, wherein said cancer cells preferably are prostate cancercells or other solid or hematological tumor cells such as lung cancer,small cell lung cancer, melanoma, liver cancer, breast cancer, Uterinecancer, Merkel cell carcinoma, pancreatic cancer, gallbladder cancer,bile duct cancer, CRC, urinary bladder cancer, non-small cell lungcancer, kidney cancer, leukemia (e.g. AML or CLL), ovarian cancer,esophageal cancer, brain cancer, and gastric (stomach) cancer, mostpreferably prostate cancer cells.

The present invention further relates to particular marker proteins andbiomarkers based on the peptides according to the present invention,herein called “targets” that can be used in the diagnosis and/orprognosis of prostate cancer. The present invention also relates to theuse of these novel targets for cancer treatment.

The term “antibody” or “antibodies” is used herein in a broad sense andincludes both polyclonal and monoclonal antibodies. In addition tointact or “full” immunoglobulin molecules, also included in the term“antibodies” are fragments (e.g. CDRs, Fv, Fab and Fc fragments) orpolymers of those immunoglobulin molecules and humanized versions ofimmunoglobulin molecules, as long as they exhibit any of the desiredproperties (e.g., specific binding of a prostate cancer marker(poly)peptide, delivery of a toxin to a prostate cancer cell expressinga cancer marker gene at an increased level, and/or inhibiting theactivity of a prostate cancer marker polypeptide) according to theinvention.

Whenever possible, the antibodies of the invention may be purchased fromcommercial sources. The antibodies of the invention may also begenerated using well-known methods. The skilled artisan will understandthat either full length prostate cancer marker polypeptides or fragmentsthereof may be used to generate the antibodies of the invention. Apolypeptide to be used for generating an antibody of the invention maybe partially or fully purified from a natural source, or may be producedusing recombinant DNA techniques.

For example, a cDNA encoding a peptide according to the presentinvention, such as a peptide according to SEQ ID No: 1 to SEQ ID No: 48polypeptide, or a variant or fragment thereof, can be expressed inprokaryotic cells (e.g., bacteria) or eukaryotic cells (e.g., yeast,insect, or mammalian cells), after which the recombinant protein can bepurified and used to generate a monoclonal or polyclonal antibodypreparation that specifically bind the prostate cancer markerpolypeptide used to generate the antibody according to the invention.

One of skill in the art will realize that the generation of two or moredifferent sets of monoclonal or polyclonal antibodies maximizes thelikelihood of obtaining an antibody with the specificity and affinityrequired for its intended use (e.g., ELISA, immunohistochemistry, invivo imaging, immunotoxin therapy). The antibodies are tested for theirdesired activity by known methods, in accordance with the purpose forwhich the antibodies are to be used (e.g., ELISA, immunohistochemistry,immunotherapy, etc.; for further guidance on the generation and testingof antibodies, see, e.g., Greenfield, 2014 (Greenfield, 2014)). Forexample, the antibodies may be tested in ELISA assays or, Western blots,immunohistochemical staining of formalin-fixed cancers or frozen tissuesections. After their initial in vitro characterization, antibodiesintended for therapeutic or in vivo diagnostic use are tested accordingto known clinical testing methods.

The term “monoclonal antibody” as used herein refers to an antibodyobtained from a substantially homogeneous population of antibodies,i.e.; the individual antibodies comprising the population are identicalexcept for possible naturally occurring mutations that may be present inminor amounts. The monoclonal antibodies herein specifically include“chimeric” antibodies in which a portion of the heavy and/or light chainis identical with or homologous to corresponding sequences in antibodiesderived from a particular species or belonging to a particular antibodyclass or subclass, while the remainder of the chain(s) is identical withor homologous to corresponding sequences in antibodies derived fromanother species or belonging to another antibody class or subclass, aswell as fragments of such antibodies, so long as they exhibit thedesired antagonistic activity (U.S. Pat. No. 4,816,567, which is herebyincorporated in its entirety).

Monoclonal antibodies of the invention may be prepared using hybridomamethods. In a hybridoma method, a mouse or other appropriate host animalis typically immunized with an immunizing agent to elicit lymphocytesthat produce or are capable of producing antibodies that willspecifically bind to the immunizing agent. Alternatively, thelymphocytes may be immunized in vitro.

The monoclonal antibodies may also be made by recombinant DNA methods,such as those described in U.S. Pat. No. 4,816,567. DNA encoding themonoclonal antibodies of the invention can be readily isolated andsequenced using conventional procedures (e.g., by using oligonucleotideprobes that are capable of binding specifically to genes encoding theheavy and light chains of murine antibodies).

In vitro methods are also suitable for preparing monovalent antibodies.Digestion of antibodies to produce fragments thereof, particularly Fabfragments, can be accomplished using routine techniques known in theart. For instance, digestion can be performed using papain. Examples ofpapain digestion are described in WO 94/29348 and U.S. Pat. No.4,342,566. Papain digestion of antibodies typically produces twoidentical antigen binding fragments, called Fab fragments, each with asingle antigen binding site, and a residual Fc fragment. Pepsintreatment yields a F(ab′)2 fragment and a pFc′ fragment.

The antibody fragments, whether attached to other sequences or not, canalso include insertions, deletions, substitutions, or other selectedmodifications of particular regions or specific amino acids residues,provided the activity of the fragment is not significantly altered orimpaired compared to the non-modified antibody or antibody fragment.These modifications can provide for some additional property, such as toremove/add amino acids capable of disulfide bonding, to increase itsbio-longevity, to alter its secretory characteristics, etc. In any case,the antibody fragment must possess a bioactive property, such as bindingactivity, regulation of binding at the binding domain, etc. Functionalor active regions of the antibody may be identified by mutagenesis of aspecific region of the protein, followed by expression and testing ofthe expressed polypeptide. Such methods are readily apparent to askilled practitioner in the art and can include site-specificmutagenesis of the nucleic acid encoding the antibody fragment.

The antibodies of the invention may further comprise humanizedantibodies or human antibodies. Humanized forms of non-human (e.g.,murine) antibodies are chimeric immunoglobulins, immunoglobulin chainsor fragments thereof (such as Fv, Fab, Fab′ or other antigen-bindingsubsequences of antibodies) which contain minimal sequence derived fromnon-human immunoglobulin. Humanized antibodies include humanimmunoglobulins (recipient antibody) in which residues from acomplementary determining region (CDR) of the recipient are replaced byresidues from a CDR of a non-human species (donor antibody) such asmouse, rat or rabbit having the desired specificity, affinity andcapacity. In some instances, Fv framework (FR) residues of the humanimmunoglobulin are replaced by corresponding non-human residues.Humanized antibodies may also comprise residues which are found neitherin the recipient antibody nor in the imported CDR or frameworksequences. In general, the humanized antibody will comprisesubstantially all of at least one, and typically two, variable domains,in which all or substantially all of the CDR regions correspond to thoseof a non-human immunoglobulin and all or substantially all of the FRregions are those of a human immunoglobulin consensus sequence. Thehumanized antibody optimally also will comprise at least a portion of animmunoglobulin constant region (Fc), typically that of a humanimmunoglobulin.

Methods for humanizing non-human antibodies are well known in the art.Generally, a humanized antibody has one or more amino acid residuesintroduced into it from a source which is non-human. These non-humanamino acid residues are often referred to as “import” residues, whichare typically taken from an “import” variable domain. Humanization canbe essentially performed by substituting rodent CDRs or CDR sequencesfor the corresponding sequences of a human antibody. Accordingly, such“humanized” antibodies are chimeric antibodies (U.S. Pat. No.4,816,567), wherein substantially less than an intact human variabledomain has been substituted by the corresponding sequence from anon-human species. In practice, humanized antibodies are typically humanantibodies in which some CDR residues and possibly some FR residues aresubstituted by residues from analogous sites in rodent antibodies.

Transgenic animals (e.g., mice) that are capable, upon immunization, ofproducing a full repertoire of human antibodies in the absence ofendogenous immunoglobulin production can be employed. For example, ithas been described that the homozygous deletion of the antibody heavychain joining region gene in chimeric and germ-line mutant mice resultsin complete inhibition of endogenous antibody production. Transfer ofthe human germ-line immunoglobulin gene array in such germ-line mutantmice will result in the production of human antibodies upon antigenchallenge. Human antibodies can also be produced in phage displaylibraries.

Antibodies of the invention are preferably administered to a subject ina pharmaceutically acceptable carrier. Typically, an appropriate amountof a pharmaceutically-acceptable salt is used in the formulation torender the formulation isotonic. Examples of thepharmaceutically-acceptable carrier include saline, Ringer's solutionand dextrose solution. The pH of the solution is preferably from about 5to about 8, and more preferably from about 7 to about 7.5. Furthercarriers include sustained release preparations such as semipermeablematrices of solid hydrophobic polymers containing the antibody, whichmatrices are in the form of shaped articles, e.g., films, liposomes ormicroparticles. It will be apparent to those persons skilled in the artthat certain carriers may be more preferable depending upon, forinstance, the route of administration and concentration of antibodybeing administered.

The antibodies can be administered to the subject, patient, or cell byinjection (e.g., intravenous, intraperitoneal, subcutaneous,intramuscular), or by other methods such as infusion that ensure itsdelivery to the bloodstream in an effective form. The antibodies mayalso be administered by intratumoral or peritumoral routes, to exertlocal as well as systemic therapeutic effects. Local or intravenousinjection is preferred.

Effective dosages and schedules for administering the antibodies may bedetermined empirically, and making such determinations is within theskill in the art. Those skilled in the art will understand that thedosage of antibodies that must be administered will vary depending on,for example, the subject that will receive the antibody, the route ofadministration, the particular type of antibody used and other drugsbeing administered. A typical daily dosage of the antibody used alonemight range from about 1 (μg/kg to up to 100 mg/kg of body weight ormore per day, depending on the factors mentioned above. Followingadministration of an antibody, preferably for treating prostate cancer,the efficacy of the therapeutic antibody can be assessed in various wayswell known to the skilled practitioner. For instance, the size, number,and/or distribution of cancer in a subject receiving treatment may bemonitored using standard tumor imaging techniques. Atherapeutically-administered antibody that arrests tumor growth, resultsin tumor shrinkage, and/or prevents the development of new tumors,compared to the disease course that would occurs in the absence ofantibody administration, is an efficacious antibody for treatment ofprostate cancer.

It is a further aspect of the invention to provide a method forproducing a soluble T-cell receptor (sTCR) recognizing a specificpeptide-MHC complex. Such soluble T-cell receptors can be generated fromspecific T-cell clones, and their affinity can be increased bymutagenesis targeting the complementarity-determining regions. For thepurpose of T-cell receptor selection, phage display can be used (US2010/0113300, (Liddy et al., 2012)). For the purpose of stabilization ofT-cell receptors during phage display and in case of practical use asdrug, alpha and beta chain can be linked e.g. by non-native disulfidebonds, other covalent bonds (single-chain T-cell receptor), or bydimerization domains (Boulter et al., 2003; Card et al., 2004; Willcoxet al., 1999). The T-cell receptor can be linked to toxins, drugs,cytokines (see, for example, US 2013/0115191), domains recruitingeffector cells such as an anti-CD3 domain, etc., in order to executeparticular functions on target cells. Moreover, it could be expressed inT cells used for adoptive transfer. Further information can be found inWO 2004/033685A1 and WO 2004/074322A1. A combination of sTCRs isdescribed in WO 2012/056407A1. Further methods for the production aredisclosed in WO 2013/057586A1.

In addition, the peptides and/or the TCRs or antibodies or other bindingmolecules of the present invention can be used to verify a pathologist'sdiagnosis of a cancer based on a biopsied sample.

The antibodies or TCRs may also be used for in vivo diagnostic assays.Generally, the antibody is labeled with a radionucleotide (such as¹¹¹In, ⁹⁹Tc, ¹⁴C, ¹³¹I, ³H, ³²P or ³⁵S) so that the tumor can belocalized using immunoscintiography. In one embodiment, antibodies orfragments thereof bind to the extracellular domains of two or moretargets of a protein selected from the group consisting of theabove-mentioned proteins, and the affinity value (Kd) is less than 1×10μM.

Antibodies for diagnostic use may be labeled with probes suitable fordetection by various imaging methods. Methods for detection of probesinclude, but are not limited to, fluorescence, light, confocal andelectron microscopy; magnetic resonance imaging and spectroscopy;fluoroscopy, computed tomography and positron emission tomography.Suitable probes include, but are not limited to, fluorescein, rhodamine,eosin and other fluorophores, radioisotopes, gold, gadolinium and otherlanthanides, paramagnetic iron, fluorine-18 and other positron-emittingradionuclides. Additionally, probes may be bi- or multi-functional andbe detectable by more than one of the methods listed. These antibodiesmay be directly or indirectly labeled with said probes. Attachment ofprobes to the antibodies includes covalent attachment of the probe,incorporation of the probe into the antibody, and the covalentattachment of a chelating compound for binding of probe, amongst otherswell recognized in the art. For immunohistochemistry, the disease tissuesample may be fresh or frozen or may be embedded in paraffin and fixedwith a preservative such as formalin. The fixed or embedded sectioncontains the sample are contacted with a labeled primary antibody andsecondary antibody, wherein the antibody is used to detect theexpression of the proteins in situ.

Another aspect of the present invention includes an in vitro method forproducing activated T cells, the method comprising contacting in vitro Tcells with antigen loaded human MHC molecules expressed on the surfaceof a suitable antigen-presenting cell for a period of time sufficient toactivate the T cell in an antigen specific manner, wherein the antigenis a peptide according to the invention. Preferably a sufficient amountof the antigen is used with an antigen-presenting cell.

Preferably the mammalian cell lacks or has a reduced level or functionof the TAP peptide transporter. Suitable cells that lack the TAP peptidetransporter include T2, RMA-S and Drosophila cells. TAP is thetransporter associated with antigen processing.

The human peptide loading deficient cell line T2 is available from theAmerican Type Culture Collection, 12301 Parklawn Drive, Rockville, Md.20852, USA under Catalogue No CRL 1992; the Drosophila cell lineSchneider line 2 is available from the ATCC under Catalogue No CRL19863; the mouse RMA-S cell line is described in Ljunggren et al.(Ljunggren and Karre, 1985).

Preferably, before transfection the host cell expresses substantially noMHC class I molecules. It is also preferred that the stimulator cellexpresses a molecule important for providing a co-stimulatory signal forT-cells such as any of B7.1, B7.2, ICAM-1 and LFA 3. The nucleic acidsequences of numerous MHC class I molecules and of the co-stimulatormolecules are publicly available from the GenBank and EMBL databases.

In case of a MHC class I epitope being used as an antigen, the T cellsare CD8-positive T cells.

If an antigen-presenting cell is transfected to express such an epitope,preferably the cell comprises an expression vector capable of expressinga peptide containing SEQ ID No: 1 to SEQ ID No: 48, or a variant aminoacid sequence thereof.

A number of other methods may be used for generating T cells in vitro.For example, autologous tumor-infiltrating lymphocytes can be used inthe generation of CTL. Plebanski et al. (Plebanski et al., 1995) madeuse of autologous peripheral blood lymphocytes (PLBs) in the preparationof T cells. Furthermore, the production of autologous T cells by pulsingdendritic cells with peptide or polypeptide, or via infection withrecombinant virus is possible. Also, B cells can be used in theproduction of autologous T cells. In addition, macrophages pulsed withpeptide or polypeptide, or infected with recombinant virus, may be usedin the preparation of autologous T cells. S. Walter et al. (Walter etal., 2003) describe the in vitro priming of T cells by using artificialantigen presenting cells (aAPCs), which is also a suitable way forgenerating T cells against the peptide of choice. In the presentinvention, aAPCs were generated by the coupling of preformed MHC:peptidecomplexes to the surface of polystyrene particles (microbeads) bybiotin:streptavidin biochemistry. This system permits the exact controlof the MHC density on aAPCs, which allows to selectively elicit high- orlow-avidity antigen-specific T cell responses with high efficiency fromblood samples. Apart from MHC:peptide complexes, aAPCs should carryother proteins with co-stimulatory activity like anti-CD28 antibodiescoupled to their surface. Furthermore such aAPC-based systems oftenrequire the addition of appropriate soluble factors, e. g. cytokines,like interleukin-12.

Allogeneic cells may also be used in the preparation of T cells and amethod is described in detail in WO 97/26328, incorporated herein byreference. For example, in addition to Drosophila cells and T2 cells,other cells may be used to present antigens such as CHO cells,baculovirus-infected insect cells, bacteria, yeast, vaccinia-infectedtarget cells. In addition plant viruses may be used (see, for example,Porta et al. (Porta et al., 1994) which describes the development ofcowpea mosaic virus as a high-yielding system for the presentation offoreign peptides.

The activated T cells that are directed against the peptides of theinvention are useful in therapy. Thus, a further aspect of the inventionprovides activated T cells obtainable by the foregoing methods of theinvention.

Activated T cells, which are produced by the above method, willselectively recognize a cell that aberrantly expresses a polypeptidethat comprises an amino acid sequence of SEQ ID No: 1 to SEQ ID No: 48.

Preferably, the T cell recognizes the cell by interacting through itsTCR with the HLA/peptide-complex (for example, binding). The T cells areuseful in a method of killing target cells in a patient whose targetcells aberrantly express a polypeptide comprising an amino acid sequenceof the invention wherein the patient is administered an effective numberof the activated T cells. The T cells that are administered to thepatient may be derived from the patient and activated as described above(i.e. they are autologous T cells). Alternatively, the T cells are notfrom the patient but are from another individual. Of course, it ispreferred if the individual is a healthy individual. By “healthyindividual” the inventors mean that the individual is generally in goodhealth, preferably has competent immune system and, more preferably, isnot suffering from any disease that can be readily tested for, anddetected.

In vivo, the target cells for the CD8-positive T cells according to thepresent invention can be cells of the tumor (which sometimes express MHCclass II) and/or stromal cells surrounding the tumor (tumor cells)(which sometimes also express MHC class II; (Dengjel et al., 2006)).

The T cells of the present invention may be used as active ingredientsof a therapeutic composition. Thus, the invention also provides a methodof killing target cells in a patient whose target cells aberrantlyexpress a polypeptide comprising an amino acid sequence of theinvention, the method comprising administering to the patient aneffective number of T cells as defined above.

By “aberrantly expressed” the inventors also mean that the polypeptideis over-expressed compared to levels of expression in normal tissues orthat the gene is silent in the tissue from which the tumor is derivedbut in the tumor it is expressed. By “over-expressed” the inventors meanthat the polypeptide is present at a level at least 1.2-fold of thatpresent in normal tissue; preferably at least 2-fold, and morepreferably at least 5-fold or 10-fold the level present in normaltissue.

T cells may be obtained by methods known in the art, e.g. thosedescribed above.

Protocols for this so-called adoptive transfer of T cells are well knownin the art. Reviews can be found in: Gattioni et al. and Morgan et al.(Gattinoni et al., 2006; Morgan et al., 2006).

Another aspect of the present invention includes the use of the peptidescomplexed with MHC to generate a T-cell receptor whose nucleic acid iscloned and is introduced into a host cell, preferably a T cell. Thisengineered T cell can then be transferred to a patient for therapy ofcancer.

Any molecule of the invention, i.e. the peptide, nucleic acid, antibody,expression vector, cell, activated T cell, T-cell receptor or thenucleic acid encoding it, is useful for the treatment of disorders,characterized by cells escaping an immune response. Therefore anymolecule of the present invention may be used as medicament or in themanufacture of a medicament. The molecule may be used by itself orcombined with other molecule(s) of the invention or (a) knownmolecule(s).

The present invention is further directed at a kit comprising:

-   (a) a container containing a pharmaceutical composition as described    above, in solution or in lyophilized form;-   (b) optionally a second container containing a diluent or    reconstituting solution for the lyophilized formulation; and-   (c) optionally, instructions for (i) use of the solution or (ii)    reconstitution and/or use of the lyophilized formulation.

The kit may further comprise one or more of (iii) a buffer, (iv) adiluent, (v) a filter, (vi) a needle, or (v) a syringe. The container ispreferably a bottle, a vial, a syringe or test tube; and it may be amulti-use container. The pharmaceutical composition is preferablylyophilized.

Kits of the present invention preferably comprise a lyophilizedformulation of the present invention in a suitable container andinstructions for its reconstitution and/or use.

Suitable containers include, for example, bottles, vials (e.g. dualchamber vials), syringes (such as dual chamber syringes) and test tubes.The container may be formed from a variety of materials such as glass orplastic. Preferably the kit and/or container contain/s instructions onor associated with the container that indicates directions forreconstitution and/or use. For example, the label may indicate that thelyophilized formulation is to be reconstituted to peptide concentrationsas described above. The label may further indicate that the formulationis useful or intended for subcutaneous administration.

The container holding the formulation may be a multi-use vial, whichallows for repeat administrations (e.g., from 2-6 administrations) ofthe reconstituted formulation. The kit may further comprise a secondcontainer comprising a suitable diluent (e.g., sodium bicarbonatesolution).

Upon mixing of the diluent and the lyophilized formulation, the finalpeptide concentration in the reconstituted formulation is preferably atleast 0.15 mg/mL/peptide (=75 μg) and preferably not more than 3mg/mL/peptide (=1500 μg). The kit may further include other materialsdesirable from a commercial and user standpoint, including otherbuffers, diluents, filters, needles, syringes, and package inserts withinstructions for use.

Kits of the present invention may have a single container that containsthe formulation of the pharmaceutical compositions according to thepresent invention with or without other components (e.g., othercompounds or pharmaceutical compositions of these other compounds) ormay have distinct container for each component.

Preferably, kits of the invention include a formulation of the inventionpackaged for use in combination with the co-administration of a secondcompound (such as adjuvants (e.g. GM-CSF), a chemotherapeutic agent, anatural product, a hormone or antagonist, an anti-angiogenesis agent orinhibitor, an apoptosis-inducing agent or a chelator) or apharmaceutical composition thereof. The components of the kit may bepre-complexed or each component may be in a separate distinct containerprior to administration to a patient. The components of the kit may beprovided in one or more liquid solutions, preferably, an aqueoussolution, more preferably, a sterile aqueous solution. The components ofthe kit may also be provided as solids, which may be converted intoliquids by addition of suitable solvents, which are preferably providedin another distinct container.

The container of a therapeutic kit may be a vial, test tube, flask,bottle, syringe, or any other means of enclosing a solid or liquid.Usually, when there is more than one component, the kit will contain asecond vial or other container, which allows for separate dosing. Thekit may also contain another container for a pharmaceutically acceptableliquid. Preferably, a therapeutic kit will contain an apparatus (e.g.,one or more needles, syringes, eye droppers, pipette, etc.), whichenables administration of the agents of the invention that arecomponents of the present kit.

The present formulation is one that is suitable for administration ofthe peptides by any acceptable route such as oral (enteral), nasal,ophthal, subcutaneous, intradermal, intramuscular, intravenous ortransdermal. Preferably, the administration is s.c., and most preferablyi.d. administration may be by infusion pump.

Since the peptides of the invention were isolated from prostate tumors,the medicament of the invention is preferably used to treat prostatetumors.

The present invention further relates to a method for producing apersonalized pharmaceutical for an individual patient comprisingmanufacturing a pharmaceutical composition comprising at least onepeptide selected from a warehouse of pre-screened TUMAPs, wherein the atleast one peptide used in the pharmaceutical composition is selected forsuitability in the individual patient. In one embodiment, thepharmaceutical composition is a vaccine. The method could also beadapted to produce T cell clones for down-stream applications, such asTCR isolations, or soluble antibodies, and other treatment options.

A “personalized pharmaceutical” shall mean specifically tailoredtherapies for one individual patient that will only be used for therapyin such individual patient, including actively personalized cancervaccines and adoptive cellular therapies using autologous patienttissue.

As used herein, the term “warehouse” shall refer to a group or set ofpeptides that have been pre-screened for immunogenicity and/orover-presentation in a particular tumor type. The term “warehouse” isnot intended to imply that the particular peptides included in thevaccine have been pre-manufactured and stored in a physical facility,although that possibility is contemplated. It is expressly contemplatedthat the peptides may be manufactured de novo for each individualizedvaccine produced, or may be pre-manufactured and stored. The warehouse(e.g. in the form of a database) is composed of tumor-associatedpeptides which were highly overexpressed in the tumor tissue of prostatecancer patients with various HLA-A HLA-B and HLA-C alleles. It maycontain MHC class I and MHC class II peptides or elongated MHC class Ipeptides. In addition to the tumor associated peptides collected fromseveral prostate tumor tissues, the warehouse may contain HLA-A*02 andHLA-A*24 marker peptides. These peptides allow comparison of themagnitude of T-cell immunity induced by TUMAPS in a quantitative mannerand hence allow important conclusion to be drawn on the capacity of thevaccine to elicit anti-tumor responses. Secondly, they function asimportant positive control peptides derived from a “non-self” antigen inthe case that any vaccine-induced T-cell responses to TUMAPs derivedfrom “self” antigens in a patient are not observed. And thirdly, it mayallow conclusions to be drawn, regarding the status of immune-competenceof the patient.

TUMAPs for the warehouse are identified by using an integratedfunctional genomics approach combining gene expression analysis, massspectrometry, and T-cell immunology (XPresident®). The approach assuresthat only TUMAPs truly present on a high percentage of tumors but not oronly minimally expressed on normal tissue, are chosen for furtheranalysis. For initial peptide selection, prostate cancer samples as wellas additional benign prostatic hyperplasia from patients and blood fromhealthy donors were analyzed in a stepwise approach:

-   1. HLA ligands from the tumorous material were identified by mass    spectrometry-   2. Genome-wide messenger ribonucleic acid (mRNA) expression analysis    was used to identify genes over-expressed in the malignant tissue    (prostate cancer) compared with a range of normal organs and tissues-   3. Identified HLA ligands were compared to gene expression data.    Peptides over-presented or selectively presented on tumor tissue,    preferably encoded by selectively expressed or over-expressed genes    as detected in step 2 were considered suitable TU MAP candidates for    a multi-peptide vaccine.-   4. Literature research was performed in order to identify additional    evidence supporting the relevance of the identified peptides as    TUMAPs-   5. The relevance of over-expression at the mRNA level was confirmed    by redetection of selected TUMAPs from step 3 on tumor tissue and    lack of (or infrequent) detection on healthy tissues.-   6. In order to assess, whether an induction of in vivo T-cell    responses by the selected peptides may be feasible, in vitro    immunogenicity assays were performed using human T cells from    healthy donors as well as from prostate cancer patients.

In an aspect, the peptides are pre-screened for immunogenicity beforebeing included in the warehouse. By way of example, and not limitation,the immunogenicity of the peptides included in the warehouse isdetermined by a method comprising in vitro T-cell priming throughrepeated stimulations of CD8+ T cells from healthy donors withartificial antigen presenting cells loaded with peptide/MHC complexesand anti-CD28 antibody.

This method is preferred for rare cancers and patients with a rareexpression profile. In contrast to multi-peptide cocktails with a fixedcomposition as currently developed, the warehouse allows a significantlyhigher matching of the actual expression of antigens in the tumor withthe vaccine. Selected single or combinations of several “off-the-shelf”peptides will be used for each patient in a multitarget approach. Intheory an approach based on selection of e.g. 5 different antigenicpeptides from a library of 50 would already lead to approximately 17million possible drug product (DP) compositions.

In an aspect, the peptides are selected for inclusion in the vaccinebased on their suitability for the individual patient based on themethod according to the present invention as described herein, or asbelow.

The HLA phenotype, transcriptomic and peptidomic data is gathered fromthe patient's tumor material, and blood samples to identify the mostsuitable peptides for each patient containing “warehouse” andpatient-unique (i.e. mutated) TUMAPs. Those peptides will be chosen,which are selectively or over-expressed in the patients tumor and, wherepossible, show strong in vitro immunogenicity if tested with thepatients' individual PBMCs.

Preferably, the peptides included in the vaccine are identified by amethod comprising: (a) identifying tumor-associated peptides (TUMAPs)presented by a tumor sample from the individual patient; (b) comparingthe peptides identified in (a) with a warehouse (database) of peptidesas described above; and (c) selecting at least one peptide from thewarehouse (database) that correlates with a tumor-associated peptideidentified in the patient. For example, the TUMAPs presented by thetumor sample are identified by: (a1) comparing expression data from thetumor sample to expression data from a sample of normal tissuecorresponding to the tissue type of the tumor sample to identifyproteins that are over-expressed or aberrantly expressed in the tumorsample; and (a2) correlating the expression data with sequences of MHCligands bound to MHC class I and/or class II molecules in the tumorsample to identify MHC ligands derived from proteins over-expressed oraberrantly expressed by the tumor. Preferably, the sequences of MHCligands are identified by eluting bound peptides from MHC moleculesisolated from the tumor sample, and sequencing the eluted ligands.Preferably, the tumor sample and the normal tissue are obtained from thesame patient.

In addition to, or as an alternative to, selecting peptides using awarehousing (database) model, TUMAPs may be identified in the patient denovo, and then included in the vaccine. As one example, candidate TUMAPsmay be identified in the patient by (a1) comparing expression data fromthe tumor sample to expression data from a sample of normal tissuecorresponding to the tissue type of the tumor sample to identifyproteins that are over-expressed or aberrantly expressed in the tumorsample; and (a2) correlating the expression data with sequences of MHCligands bound to MHC class I and/or class II molecules in the tumorsample to identify MHC ligands derived from proteins over-expressed oraberrantly expressed by the tumor. As another example, proteins may beidentified containing mutations that are unique to the tumor samplerelative to normal corresponding tissue from the individual patient, andTUMAPs can be identified that specifically target the mutation. Forexample, the genome of the tumor and of corresponding normal tissue canbe sequenced by whole genome sequencing: For discovery of non-synonymousmutations in the protein-coding regions of genes, genomic DNA and RNAare extracted from tumor tissues and normal non-mutated genomic germlineDNA is extracted from peripheral blood mononuclear cells (PBMCs). Theapplied NGS approach is confined to the re-sequencing of protein codingregions (exome re-sequencing). For this purpose, exonic DNA from humansamples is captured using vendor-supplied target enrichment kits,followed by sequencing with e.g. a HiSeq2000 (Illumina). Additionally,tumor mRNA is sequenced for direct quantification of gene expression andvalidation that mutated genes are expressed in the patients' tumors. Theresultant millions of sequence reads are processed through softwarealgorithms. The output list contains mutations and gene expression.Tumor-specific somatic mutations are determined by comparison with thePBMC-derived germline variations and prioritized. The de novo identifiedpeptides can then be tested for immunogenicity as described above forthe warehouse, and candidate TUMAPs possessing suitable immunogenicityare selected for inclusion in the vaccine.

In one exemplary embodiment, the peptides included in the vaccine areidentified by: (a) identifying tumor-associated peptides (TUMAPs)presented by a tumor sample from the individual patient by the method asdescribed above; (b) comparing the peptides identified in a) with awarehouse of peptides that have been prescreened for immunogenicity andoverpresentation in tumors as compared to corresponding normal tissue;(c) selecting at least one peptide from the warehouse that correlateswith a tumor-associated peptide identified in the patient; and (d)optionally, selecting at least one peptide identified de novo in (a)confirming its immunogenicity.

In one exemplary embodiment, the peptides included in the vaccine areidentified by: (a) identifying tumor-associated peptides (TUMAPs)presented by a tumor sample from the individual patient; and (b)selecting at least one peptide identified de novo in (a) and confirmingits immunogenicity.

Once the peptides for a personalized peptide based vaccine are selected,the vaccine is produced. The vaccine preferably is a liquid formulationconsisting of the individual peptides dissolved in between 20-40% DMSO,preferably about 30-35% DMSO, such as about 33% DMSO.

Each peptide to be included into a product is dissolved in DMSO. Theconcentration of the single peptide solutions has to be chosen dependingon the number of peptides to be included into the product. The singlepeptide-DMSO solutions are mixed in equal parts to achieve a solutioncontaining all peptides to be included in the product with aconcentration of ˜2.5 mg/ml per peptide. The mixed solution is thendiluted 1:3 with water for injection to achieve a concentration of 0.826mg/ml per peptide in 33% DMSO. The diluted solution is filtered througha 0.22 μm sterile filter. The final bulk solution is obtained.

Final bulk solution is filled into vials and stored at −20° C. untiluse. One vial contains 700 μL solution, containing 0.578 mg of eachpeptide. Of this, 500 μL (approx. 400 μg per peptide) will be appliedfor intradermal injection.

In addition to being useful for treating cancer, the peptides of thepresent invention are also useful as diagnostics. Since the peptideswere generated from prostate tumor cells and since it was determinedthat these peptides are not or at lower levels present in normaltissues, these peptides can be used to diagnose the presence of a tumor.

The presence of claimed peptides on tissue biopsies in blood samples canassist a pathologist in diagnosis of cancer. Detection of certainpeptides by means of antibodies, mass spectrometry or other methodsknown in the art can tell the pathologist that the tissue sample ismalignant or inflamed or generally diseased, or can be used as abiomarker for prostate cancer. Presence of groups of peptides can enableclassification or sub-classification of diseased tissues.

The detection of peptides on diseased tissue specimen can enable thedecision about the benefit of therapies involving the immune system,especially if T-lymphocytes are known or expected to be involved in themechanism of action. Loss of MHC expression is a well describedmechanism by which infected of malignant cells escapeimmuno-surveillance. Thus, presence of peptides shows that thismechanism is not exploited by the analyzed cells.

The peptides of the present invention might be used to analyzelymphocyte responses against those peptides such as T cell responses orantibody responses against the peptide or the peptide complexed to MHCmolecules. These lymphocyte responses can be used as prognostic markersfor decision on further therapy steps. These responses can also be usedas surrogate response markers in immunotherapy approaches aiming toinduce lymphocyte responses by different means, e.g. vaccination ofprotein, nucleic acids, autologous materials, adoptive transfer oflymphocytes. In gene therapy settings, lymphocyte responses againstpeptides can be considered in the assessment of side effects. Monitoringof lymphocyte responses might also be a valuable tool for follow-upexaminations of transplantation therapies, e.g. for the detection ofgraft versus host and host versus graft diseases.

The present invention will now be described in the following exampleswhich describe preferred embodiments thereof, and with reference to theaccompanying figures, nevertheless, without being limited thereto. Forthe purposes of the present invention, all references as cited hereinare incorporated by reference in their entireties.

FIGURES

FIGS. 1A-C show the over-presentation of various peptides in normaltissues (white bars) and prostate cancer tissues and benign prostatehyperplasia tissues (black bars). FIGS. 1D-E show all cell lines, normaltissues and cancers tissues where the exemplary peptides (SLLSHQVLL(A*02) (SEQ ID NO. 20) and SLLSHQVLL (A*24) (SEQ ID NO. 20)) has beendetected. FIG. 1A) Gene: OR51E2, Peptide: VTAQIGIVAV (A*02; SEQ IDNO.:1)—Tissues from left to right: 1 adipose tissues, 3 adrenal glands,6 arteries, 5 bone marrows, 7 brains, 3 breasts, 1 central nerve, 13colons, 1 duodenum, 8 esophagi, 2 gallbladders, 5 hearts, 16 kidneys, 21livers, 46 lungs, 4 lymph nodes, 4 leukocyte samples, 4 ovaries, 7pancreas, 4 peripheral nerves, 1 peritoneum, 3 pituitary glands, 4placentas, 3 pleuras, 6 recti, 7 salivary glands, 4 skeletal muscles, 6skins, 2 small intestines, 4 spleens, 7 stomachs, 4 testis, 3 thymi, 4thyroid glands, 10 tracheas, 3 ureters, 6 urinary bladders, 2 uteri, 2veins, 3 prostate, 44 tumorous prostates. The peptide was also found onsmall cell lung cancer (not shown). FIG. 1B) Gene: MANSC1, Peptide:KMDEASAQLL (A*02; SEQ ID NO.:14)—Tissues from left to right: 1 adiposetissues, 3 adrenal glands, 6 arteries, 5 bone marrows, 7 brains, 3breasts, 1 central nerve, 13 colons, 1 duodenum, 8 esophagi, 2gallbladders, 5 hearts, 16 kidneys, 21 livers, 46 lungs, 4 lymph nodes,4 leukocyte samples, 4 ovaries, 7 pancreas, 4 peripheral nerves, 1peritoneum, 3 pituitary glands, 4 placentas, 3 pleuras, 6 recti, 7salivary glands, 4 skeletal muscles, 6 skins, 2 small intestines, 4spleens, 7 stomachs, 4 testis, 3 thymi, 4 thyroid glands, 10 tracheas, 3ureters, 6 urinary bladders, 2 uteri, 2 veins, 3 prostate, 44 tumorousprostates. FIG. 1C) Gene: TRPM8, Peptide: SYNDALLTF (A*24; SEQ IDNO.:24)—Tissues from left to right: 2 adrenal glands, 1 artery, 4brains, 1 breast, 5 colons, 1 heart, 13 kidneys, 9 livers, 9 lungs, 3pancreas, 1 pituitary gland, 2 recti, 3 skins, 1 spleen, 12 stomachs, 1thymus, 2 uteri, 40 tumorous prostates. The peptide was also found onnon-small cell lung cancer (not shown). FIG. 1D) Gene: KIAA1244,Peptide: SLLSHQVLL (A*02; SEQ ID NO.:20)—Tissues from left to right: 1pancreatic cell line, 20 cancer tissues (1 brain cancer, 1 breastcancer, 2 colon cancers, 1 esophageal cancer, 1 kidney cancer, 1 livercancer, 3 lung cancers, 8 prostate cancers, 1 stomach cancer, 1 urinarybladder cancer). The set of normal tissues was the same as in A-B, butthe peptide was not detected on any normal tissue. FIG. 1E) Gene:KIAA1244, Peptide: QYGKDFLTL (A*24; SEQ ID NO.:33)—Tissues from left toright: 3 benign prostate hyperplasia tissues, 3 normal tissues (1 liver,1 lung, 1 rectum), 31 cancer tissues (5 brain cancers, 4 liver cancers,15 lung cancers, 7 prostate cancers). The set of normal tissues was thesame as in C, but tissues without detection are not shown. FIGS. 1F-Kshow the over-presentation of various peptides in normal tissues (whitebars) and prostate cancer tissues and benign prostate hyperplasiatissues (black bars). FIG. 1L-S show all cell lines, normal tissues andcancers tissues where various peptides have been detected. FIG. 1F)Gene: NEFH, Peptide: HLLEDIAHV (A*02; SEQ ID NO.: 3)—Tissues from leftto right: 1 adipose tissue, 3 adrenal glands, 6 arteries, 5 bonemarrows, 7 brains, 3 breasts, 1 central nerve, 13 colons, 1 duodenum, 8esophagi, 2 gallbladders, 5 hearts, 16 kidneys, 4 leukocyte samples, 21livers, 46 lungs, 4 lymph nodes, 3 ovaries, 7 pancreases, 4 peripheralnerves, 1 peritoneum, 3 pituitary glands, 2 placentas, 3 pleuras, 6rectums, 7 salivary glands, 4 skeletal muscles, 5 skins, 2 smallintestines, 4 spleens, 7 stomachs, 4 testes, 3 thymi, 4 thyroid glands,9 tracheas, 3 ureters, 6 urinary bladders, 2 uteri, 2 veins, 3prostates, 33 prostate cancer tissues and 10 benign prostate hyperplasiatissues. FIG. 1G) Gene: PDE11A, Peptide: ALLESRVNL (A*02; SEQ ID NO.:6)—Tissues from left to right: 1 adipose tissue, 3 adrenal glands, 6arteries, 5 bone marrows, 7 brains, 3 breasts, 1 central nerve, 13colons, 1 duodenum, 8 esophagi, 2 gallbladders, 5 hearts, 16 kidneys, 4leukocyte samples, 21 livers, 46 lungs, 4 lymph nodes, 3 ovaries, 7pancreases, 4 peripheral nerves, 1 peritoneum, 3 pituitary glands, 2placentas, 3 pleuras, 6 rectums, 7 salivary glands, 4 skeletal muscles,5 skins, 2 small intestines, 4 spleens, 7 stomachs, 4 testes, 3 thymi, 4thyroid glands, 9 tracheas, 3 ureters, 6 urinary bladders, 2 uteri, 2veins, 3 prostates, 33 prostate cancer tissues and 10 benign prostatehyperplasia tissues. FIG. 1H) Gene: KLK4, Peptide: GYLQGLVSF (A*24; SEQID NO.: 27)—Tissues from left to right: 2 adrenal glands, 1 artery, 4brains, 1 breast, 5 colons, 1 heart, 13 kidneys, 9 livers, 9 lungs, 3pancreases, 1 pituitary gland, 2 rectums, 3 skins, 1 spleen, 12stomachs, 1 thymus, 2 uteri, 37 prostate cancer tissues and 3 benignprostate hyperplasia tissues. FIG. 1I) Gene: TGFB3, Peptide: YYAKEIHKF(A*24; SEQ ID NO.: 28)—Tissues from left to right: 2 adrenal glands, 1artery, 4 brains, 1 breast, 5 colons, 1 heart, 13 kidneys, 9 livers, 9lungs, 3 pancreases, 1 pituitary gland, 2 rectums, 3 skins, 1 spleen, 12stomachs, 1 thymus, 2 uteri, 37 prostate cancer tissues and 3 benignprostate hyperplasia tissues. FIG. 1J) Gene: KLK3, Peptide: SLFHPEDTGQV(A*02; SEQ ID NO.: 49)—Tissues from left to right: 1 adipose tissue, 3adrenal glands, 6 arteries, 5 bone marrows, 7 brains, 3 breasts, 1central nerve, 13 colons, 1 duodenum, 8 esophagi, 2 gallbladders, 5hearts, 16 kidneys, 4 leukocyte samples, 21 livers, 46 lungs, 4 lymphnodes, 3 ovaries, 7 pancreases, 4 peripheral nerves, 1 peritoneum, 3pituitary glands, 2 placentas, 3 pleuras, 6 rectums, 7 salivary glands,4 skeletal muscles, 5 skins, 2 small intestines, 4 spleens, 7 stomachs,4 testes, 3 thymi, 4 thyroid glands, 9 tracheas, 3 ureters, 6 urinarybladders, 2 uteri, 2 veins, 3 prostates, 33 prostate cancer tissues and10 benign prostate hyperplasia tissues. FIG. 1K) Gene: KLK2, Peptide:AYSEKVTEF (A*24; SEQ ID NO.: 54)—Tissues from left to right: 2 adrenalglands, 1 artery, 4 brains, 1 breast, 5 colons, 1 heart, 13 kidneys, 9livers, 9 lungs, 3 pancreases, 1 pituitary gland, 2 rectums, 3 skins, 1spleen, 12 stomachs, 1 thymus, 2 uteri, 37 prostate cancer tissues and 3benign prostate hyperplasia tissues. FIG. 1L) Gene: GREB1, Peptide:SMLGEEIQL (A*02; SEQ ID NO.: 2)—Tissues from left to right: 1 benignprostate hyperplasia tissue (BPH), 3 cell-lines (3 skins), 1 normaltissue (1 uterus), 26 cancer tissues (2 breast cancers, 2 liver cancers,1 lung cancer, 1 ovarian cancer, 13 prostate cancers, 6 skin cancers, 1uterus cancer. FIG. 1M) Gene: TRPM8, Peptide: ALLTFVWKL (A*02; SEQ IDNO.: 4)—Tissues from left to right: 3 benign prostate hyperplasiatissues (BPH), 13 cancer tissues (1 brain cancer, 12 prostate cancers).FIG. 1N) Gene: TRPM8, Peptide: KIFSRLIYI (A*02; SEQ ID NO.: 5)—Tissuesfrom left to right: 4 benign prostate hyperplasia tissues (BPH), 10cancer tissues (1 brain cancer, 8 prostate cancers, 1 skin cancer). FIG.1O) Gene: MANSC1, Peptide: KMDEASAQL (A*02; SEQ ID NO.: 16)—Tissues fromleft to right: 21 cancer tissues (20 prostate cancers, 1 urinary bladdercancer). FIG. 1P) Gene: C6orf132, Peptide: RYGSPINTF (A*24; SEQ ID NO.:29)—Tissues from left to right: 4 benign prostate hyperplasia tissues(BPH), 54 cancer tissues (1 liver cancer, 24 lung cancers, 26 prostatecancers, 3 stomach cancers). FIG. 1Q) Gene: ITGA7, Peptide: AFSPDSHYLLF(A*24; SEQ ID NO.: 34)—Tissues from left to right: 5 benign prostatehyperplasia tissues (BPH), 44 cancer tissues (10 brain cancers, 1 kidneycancer, 4 liver cancers, 18 lung cancers, 11 prostate cancers). FIG. 1R)Gene: TPSB2, TPSAB1, Peptide: IYTRVTYYL (A*24; SEQ ID NO.: 35)—Tissuesfrom left to right: 3 benign prostate hyperplasia tissues (BPH), 59cancer tissues (36 lung cancers, 14 prostate cancers, 9 stomachcancers). FIG. 1S) Gene: SLC30A4, Peptide: ALGDLVQSV (A*02; SEQ ID NO.:52)—Tissues from left to right: 1 benign prostate hyperplasia tissues(BPH), 11 cancer tissues (1 lymph node cancer, 9 prostate cancers, 1skin cancer).

FIGS. 2A to E show exemplary expression profiles (relative expressioncompared to normal kidney) of source genes of the present invention thatare highly over-expressed or exclusively expressed in prostate cancer ina panel of normal tissues and 20 prostate cancer samples. Tissues fromleft to right: adrenal gland, artery, bone marrow, brain (whole),breast, colon, esophagus, heart, kidney (triplicate), leukocytes, liver,lung, lymph node, ovary, pancreas, placenta, prostate, salivary gland,skeletal muscle, skin, small intestine, spleen, stomach, testis, thymus,thyroid gland, urinary bladder, uterine cervix, uterus, vein, 20prostate cancer samples. FIG. 2A) NEFH; FIG. 2B) ABCC4; FIG. 2C) RAB3B;FIG. 2D) OR51E2; and FIG. 2E) KLK2.

FIG. 3 shows exemplary immunogenicity data: flow cytometry results afterpeptide-specific multimer staining. A) TYIGQGYII (FKBP10; SEQ ID No.42); B) IYTRVTYYL (TPSB2, TPSAB1; SEQ ID No. 35).

FIG. 4A to C show exemplary results of peptide-specific in vitro CD8+ Tcell responses of a healthy HLA-A*02+ donor. CD8+ T cells were primedusing artificial APCs coated with anti-CD28 mAb and HLA-A*02 in complexwith SeqID No 1 peptide (A, left panel), SeqID No 3 peptide (B, leftpanel) or SeqID No 5 peptide (C, left panel), respectively. After threecycles of stimulation, the detection of peptide-reactive cells wasperformed by 2D multimer staining with A*02/SeqID No 1 (A), A*02/SeqIDNo 3 (B) or A*02/SeqID No 5 (C). Right panels (A, B and C) show controlstaining of cells stimulated with irrelevant A*02/peptide complexes.Viable singlet cells were gated for CD8+ lymphocytes. Boolean gateshelped excluding false-positive events detected with multimers specificfor different peptides. Frequencies of specific multimer+ cells amongCD8+ lymphocytes are indicated.

FIG. 5A to B show exemplary results of peptide-specific in vitro CD8+ Tcell responses of a healthy HLA-A*24+ donor. CD8+ T cells were primedusing artificial APCs coated with anti-CD28 mAb and HLA-A*24 in complexwith SeqID No 24 peptide (A, left panel) or SeqID No 27 peptide (B, leftpanel), respectively. After three cycles of stimulation, the detectionof peptide-reactive cells was performed by 2D multimer staining withA*24/SeqID No 24 (A), or A*24/SeqID No 27 (B). Right panels (A, and B)show control staining of cells stimulated with irrelevant A*24/peptidecomplexes. Viable singlet cells were gated for CD8+ lymphocytes. Booleangates helped excluding false-positive events detected with multimersspecific for different peptides. Frequencies of specific multimer+ cellsamong CD8+ lymphocytes are indicated.

EXAMPLES Example 1

Identification and Quantitation of Tumor Associated Peptides Presentedon the Cell Surface

Tissue Samples

Patients' prostate tumor tissues were obtained from Asterand (Detroit,USA and Royston, Herts, UK); BioServe (Beltsville, Md., USA); GeneticistInc. (Glendale, Calif., USA); Indivumed GmbH (Hamburg, Germany); SaintSavas Hospital, Athens, Greece, University Hospital of Tubingen. Normaltissues were obtained from Asterand (Detroit, USA and Royston, Herts,UK); Bio-Options Inc, CA, USA; BioServe, Beltsville, Md., USA; CapitalBioScience Inc, Rockville, Md., USA; Geneticist Inc., Glendale, Calif.,USA; University Hospital of Geneva; University Hospital of Heidelberg;Kyoto Prefectural University of Medicine (KPUM); Osaka City University(OCU); University Hospital Munich; ProteoGenex Inc., Culver City,Calif., USA; Tissue Solutions Ltd., Glasgow, United Kingdom; UniversityHospital of Tubingen. Written informed consents of all patients had beengiven before surgery or autopsy. Tissues were shock-frozen immediatelyafter excision and stored until isolation of TUMAPs at −70° C. or below.

Isolation of HLA Peptides from Tissue Samples

HLA peptide pools from shock-frozen tissue samples were obtained byimmune precipitation from solid tissues according to a slightly modifiedprotocol (Falk et al., 1991; Seeger et al., 1999) using theHLA-A*02-specific antibody BB7.2, the HLA-A, -B, C-specific antibodyW6/32, CNBr-activated sepharose, acid treatment, and ultrafiltration.

Mass Spectrometry Analyses

The HLA peptide pools as obtained were separated according to theirhydrophobicity by reversed-phase chromatography (nanoAcquity UPLCsystem, Waters) and the eluting peptides were analyzed in LTQ-velos andfusion hybrid mass spectrometers (ThermoElectron) equipped with an ESIsource. Peptide pools were loaded directly onto the analyticalfused-silica micro-capillary column (75 μm i.d.×250 mm) packed with 1.7μm C18 reversed-phase material (Waters) applying a flow rate of 400 nLper minute. Subsequently, the peptides were separated using a two-step180 minute-binary gradient from 10% to 33% B at a flow rate of 300 nLper minute. The gradient was composed of Solvent A (0.1% formic acid inwater) and solvent B (0.1% formic acid in acetonitrile). A gold coatedglass capillary (PicoTip, New Objective) was used for introduction intothe nanoESI source. The LTQ-Orbitrap mass spectrometers were operated inthe data-dependent mode using a TOPS strategy. In brief, a scan cyclewas initiated with a full scan of high mass accuracy in the orbitrap(R=30 000), which was followed by MS/MS scans also in the orbitrap(R=7500) on the 5 most abundant precursor ions with dynamic exclusion ofpreviously selected ions. Tandem mass spectra were interpreted bySEQUEST and additional manual control. The identified peptide sequencewas assured by comparison of the generated natural peptide fragmentationpattern with the fragmentation pattern of a synthetic sequence-identicalreference peptide.

Label-free relative LC-MS quantitation was performed by ion countingi.e. by extraction and analysis of LC-MS features (Mueller et al.,2007). The method assumes that the peptide's LC-MS signal areacorrelates with its abundance in the sample. Extracted features werefurther processed by charge state deconvolution and retention timealignment (Mueller et al., 2008; Sturm et al., 2008). Finally, all LC-MSfeatures were cross-referenced with the sequence identification resultsto combine quantitative data of different samples and tissues to peptidepresentation profiles. The quantitative data were normalized in atwo-tier fashion according to central tendency to account for variationwithin technical and biological replicates. Thus each identified peptidecan be associated with quantitative data allowing relativequantification between samples and tissues. In addition, allquantitative data acquired for peptide candidates was inspected manuallyto assure data consistency and to verify the accuracy of the automatedanalysis. For each peptide a presentation profile was calculated showingthe mean sample presentation as well as replicate variations. Theprofiles juxtapose prostate cancer samples and benign prostatehyperplasia samples to a baseline of normal tissue samples. Presentationprofiles of exemplary over-presented peptides are shown in FIG. 1.Presentation scores for exemplary peptides are shown in Table 12 andTable 13.

TABLE 12 Presentation scores. The table lists HLA-A*02peptides that are very highly over-presentedon tumors compared to a panel of normal tissues(+++), highly over-presented on tumors comparedto a panel of normal tissues (++) or over-presented on tumors compared to a panel of normal tissues (+). SEQ IDNo. Sequence Peptide Presentation  1 VTAQIGIVAV +++  2 SMLGEEIQL +++  3HLLEDIAHV +++  4 ALLTFVWKL +++  5 KIFSRLIYI +++  6 ALLESRVNL +++  7TLLQVVGVVSV +++  8 LLDFSLADA +++  9 GMLNEAEGKAIKL ++ 10 TLWRGPVVV +++ 11YLEEECPAT +++ 12 SLNEEIAFL +++ 14 KMDEASAQLL +++ 15 KMDEASAQLLA +++ 17RLGIKPESV ++ 18 GLSEFTEYL +++ 19 LLPPPPLLA +++ 20 SLLSHQVLL +++ 21YLNDSLRHV +++ 22 SLYDSIAFI +++ 23 AVAGADVIITV + 40 RTFJPTYGL ++

TABLE 13 Presentation scores. The table lists HLA-A*24peptides that are very highly over-presentedon tumors compared to a panel of normal tissues(+++), highly over-presented on tumors comparedto a panel of normal tissues (++) or over-presented on tumors compared to a panel of normal tissues (+). SEQ IDNo. Sequence Peptide Presentation 24 SYNDALLTF +++ 25 IYEPYLAMF + 26RYADDTFTPAF +++ 27 GYLQGLVSF +++ 28 YYAKEIHKF +++ 29 RYGSPINTF +++ 30SYSPAHARL +++ 31 AYTSPPSFF +++ 32 PYQLNASLFTF +++ 34 AFSPDSHYLLF +++ 35IYTRVTYYL +++ 36 RYMWINQEL ++ 37 RYLQDLLAW +++ 38 VYSDKLWIF ++ 39SYIDVAVKL + 41 RYLQKIEEF +++ 42 TYIGQGYII +++ 43 AYIKNGQLF +++ 44VYNTVSEGTHF + 45 RYFKTPRKF ++ 46 VYEEILHQI ++ 47 SYTPVLNQF ++ 48AWAPKPYHKF ++

Example 2

Expression Profiling of Genes Encoding the Peptides of the Invention

Over-presentation or specific presentation of a peptide on tumor cellscompared to normal cells is sufficient for its usefulness inimmunotherapy, and some peptides are tumor-specific despite their sourceprotein occurring also in normal tissues. Still, mRNA expressionprofiling adds an additional level of safety in selection of peptidetargets for immunotherapies. Especially for therapeutic options withhigh safety risks, such as affinity-matured TCRs, the ideal targetpeptide will be derived from a protein that is unique to the tumor andnot found on normal tissues.

RNA Sources and Preparation

Surgically removed tissue specimens were provided as indicated above(see Example 1) after written informed consent had been obtained fromeach patient. Tumor tissue specimens were snap-frozen immediately aftersurgery and later homogenized with mortar and pestle under liquidnitrogen. Total RNA was prepared from these samples using TRI Reagent(Ambion, Darmstadt, Germany) followed by a cleanup with RNeasy (QIAGEN,Hilden, Germany); both methods were performed according to themanufacturer's protocol.

Total RNA from healthy human tissues was obtained commercially (Ambion,Huntingdon, UK; Clontech, Heidelberg, Germany; Stratagene, Amsterdam,Netherlands; Bio-Chain, Hayward, Calif., USA). The RNA from severalindividuals (between 2 and 123 individuals) was mixed such that RNA fromeach individual was equally weighted.

Quality and quantity of all RNA samples were assessed on an Agilent 2100Bioanalyzer (Agilent, Waldbronn, Germany) using the RNA 6000 PicoLabChip Kit (Agilent).

Microarray Experiments

Gene expression analysis of all tumor and normal tissue RNA samples wasperformed by Affymetrix Human Genome (HG) U133A or HG-U133 Plus 2.0oligonucleotide microarrays (Affymetrix, Santa Clara, Calif., USA). Allsteps were carried out according to the Affymetrix manual. Briefly,double-stranded cDNA was synthesized from 5-8 μg of total RNA, usingSuperScript RTII (Invitrogen) and the oligo-dT-T7 primer (MWG Biotech,Ebersberg, Germany) as described in the manual. In vitro transcriptionwas performed with the BioArray High Yield RNA Transcript Labelling Kit(ENZO Diagnostics, Inc., Farmingdale, N.Y., USA) for the U133A arrays orwith the GeneChip IVT Labelling Kit (Affymetrix) for the U133 Plus 2.0arrays, followed by cRNA fragmentation, hybridization, and staining withstreptavidin-phycoerythrin and biotinylated anti-streptavidin antibody(Molecular Probes, Leiden, Netherlands). Images were scanned with theAgilent 2500A GeneArray Scanner (U133A) or the Affymetrix Gene-ChipScanner 3000 (U133 Plus 2.0), and data were analyzed with the GCOSsoftware (Affymetrix), using default settings for all parameters. Fornormalization, 100 housekeeping genes provided by Affymetrix were used.Relative expression values were calculated from the signal log ratiosgiven by the software and the normal kidney sample was arbitrarily setto 1.0. Exemplary expression profiles of source genes of the presentinvention that are highly over-expressed or exclusively expressed inprostate cancer are shown in FIGS. 2A to E. Expression scores forfurther exemplary genes are shown in Table 14.

TABLE 14 Expression scores. The table lists peptides fromgenes that are very highly over-expressed intumors compared to a panel of normal tissues(+++), highly over-expressed in tumors comparedto a panel of normal tissues (++) or over-expressed in tumors compared to a panel of normal tissues (+). SEQ ID NoSequence Gene Expression  1 VTAQIGIVAV ++  2 SMLGEEIQL ++  3 HLLEDIAHV+++  4 ALLTFVWKL +  5 KIFSRLIYI +  7 TLLQVVGVVSV ++ 11 YLEEECPAT + 19LLPPPPLLA + 24 SYNDALLTF + 25 IYEPYLAMF + 26 RYADDTFTPAF ++ 28YYAKEIHKF + 44 VYNTVSEGTHF ++

Example 3

In Vitro Immunogenicity for MHC Class I Presented Peptides

In order to obtain information regarding the immunogenicity of theTUMAPs of the present invention, the inventors performed investigationsusing an in vitro T-cell priming assay based on repeated stimulations ofCD8+ T cells with artificial antigen presenting cells (aAPCs) loadedwith peptide/MHC complexes and anti-CD28 antibody. This way theinventors could show for some selected TUMAPs immunogenicity forHLA-A*0201 restricted and HLA-A*24 restricted TUMAPs of the invention,demonstrating that these peptides are T-cell epitopes against which CD8+precursor T cells exist in humans (Table 15 A+B).

In Vitro Priming of CD8+ T Cells

In order to perform in vitro stimulations by artificial antigenpresenting cells loaded with peptide-MHC complex (pMHC) and anti-CD28antibody, the inventors first isolated CD8+ T cells from fresh HLA-A*02leukapheresis products via positive selection using CD8 microbeads(Miltenyi Biotec, Bergisch-Gladbach, Germany) of healthy donors obtainedfrom the University clinics Mannheim, Germany, after informed consent.

PBMCs and isolated CD8+ lymphocytes were incubated in T-cell medium(TCM) until use consisting of RPMI-Glutamax (Invitrogen, Karlsruhe,Germany) supplemented with 10% heat inactivated human AB serum(PAN-Biotech, Aidenbach, Germany), 100 U/ml Penicillin/100 μg/mlStreptomycin (Cambrex, Cologne, Germany), 1 mM sodium pyruvate (CC Pro,Oberdorla, Germany), 20 μg/ml Gentamycin (Cambrex). 2.5 ng/ml IL-7(PromoCell, Heidelberg, Germany) and 10 U/ml IL-2 (Novartis Pharma,Nürnberg, Germany) were also added to the TCM at this step.

Generation of pMHC/anti-CD28 coated beads, T-cell stimulations andreadout was performed in a highly defined in vitro system using fourdifferent pMHC molecules per stimulation condition and 8 different pMHCmolecules per readout condition.

The purified co-stimulatory mouse IgG2a anti human CD28 Ab 9.3 (Jung etal., 1987) was chemically biotinylated usingSulfo-N-hydroxysuccinimidobiotin as recommended by the manufacturer(Perbio, Bonn, Germany). Beads used were 5.6 μm diameter streptavidincoated polystyrene particles (Bangs Laboratories, Illinois, USA).

pMHC used for positive and negative control stimulations wereA*0201/MLA-001 (peptide ELAGIGILTV (SEQ ID No. 60) from modifiedMelan-A/MART-1) and A*0201/DDX5-001 (YLLPAIVHI from DDX5, SEQ ID No.61), respectively.

800.000 beads/200 μl were coated in 96-well plates in the presence of4×12.5 ng different biotin-pMHC, washed and 600 ng biotin anti-CD28 wereadded subsequently in a volume of 200 μl. Stimulations were initiated in96-well plates by co-incubating 1×10⁶ CD8+ T cells with 2×10⁵ washedcoated beads in 200 μl TCM supplemented with 5 ng/ml IL-12 (PromoCell)for 3 days at 37° C. Half of the medium was then exchanged by fresh TCMsupplemented with 80 U/ml IL-2 and incubating was continued for 4 daysat 37° C. This stimulation cycle was performed for a total of threetimes. For the pMHC multimer readout using 8 different pMHC moleculesper condition, a two-dimensional combinatorial coding approach was usedas previously described (Andersen et al., 2012) with minor modificationsencompassing coupling to 5 different fluorochromes. Finally, multimericanalyses were performed by staining the cells with Live/dead near IR dye(Invitrogen, Karlsruhe, Germany), CD8-FITC antibody clone SK1 (BD,Heidelberg, Germany) and fluorescent pMHC multimers. For analysis, a BDLSRII SORP cytometer equipped with appropriate lasers and filters wasused. Peptide specific cells were calculated as percentage of total CD8+cells. Evaluation of multimeric analysis was done using the FlowJosoftware (Tree Star, Oregon, USA). In vitro priming of specificmultimer+ CD8+ lymphocytes was detected by comparing to negative controlstimulations. Immunogenicity for a given antigen was detected if atleast one evaluable in vitro stimulated well of one healthy donor wasfound to contain a specific CD8+ T-cell line after in vitro stimulation(i.e. this well contained at least 1% of specific multimer+ among CD8+T-cells and the percentage of specific multimer+ cells was at least 10×the median of the negative control stimulations).

In Vitro Immunogenicity for Prostate Cancer Peptides

For tested HLA class I peptides, in vitro immunogenicity could bedemonstrated by generation of peptide specific T-cell lines. Exemplaryflow cytometry results after TUMAP-specific multimer staining for 2peptides of the invention are shown in FIG. 3 together withcorresponding negative controls. Results for 5 peptides from theinvention are summarized in Table 15A. Further results for 6 peptidesfrom the invention are summarized in Table 15B.

TABLE 15A in vitro immunogenicity of HLA class I peptidesof the invention Exemplary results of in vitroimmunogenicity experiments conducted by theapplicant for the peptides of the invention. <20% = +; 20%-49% =++; 50%-69% = +++;  > = 70% = ++++ Seq ID Sequence wells donors 17RLGIKPESV ++ ++++ 29 RYGSPINTF + +++ 34 AFSPDSHYLLF + +++ 35 IYTRVTYYL++ ++++ 42 TYIGQGYII + ++++

TABLE 15B in vitro immunogenicity of HLA class I peptidesof the invention Exemplary results of in vitroimmunogenicity experiments conducted by theapplicant for the peptides of the invention. >20% = +; 20%-49% =++; 50%-69 % = +++; > = 70% = ++++ SEQ ID Sequence Wells positive [%]  1VTAQIGIVAV ++++  3 HLLEDIAHV ++  5 KIFSRLIYI +++  6 ALLESRVNL + 24SYNDALLTF +++ 27 GYLQGLVSF ++

Example 4

Synthesis of Peptides

All peptides were synthesized using standard and well-established solidphase peptide synthesis using the Fmoc-strategy. Identity and purity ofeach individual peptide have been determined by mass spectrometry andanalytical RP-HPLC. The peptides were obtained as white to off-whitelyophilizates (trifluoro acetate salt) in purities of >50%. All TUMAPsare preferably administered as trifluoro-acetate salts or acetate salts,other salt-forms are also possible.

Example 5

MHC Binding Assays

Candidate peptides for T cell based therapies according to the presentinvention were further tested for their MHC binding capacity (affinity).The individual peptide-MHC complexes were produced by UV-ligandexchange, where a UV-sensitive peptide is cleaved upon UV-irradiation,and exchanged with the peptide of interest as analyzed. Only peptidecandidates that can effectively bind and stabilize the peptide-receptiveMHC molecules prevent dissociation of the MHC complexes. To determinethe yield of the exchange reaction, an ELISA was performed based on thedetection of the light chain ((32m) of stabilized MHC complexes. Theassay was performed as generally described in Rodenko et al. (Rodenko etal., 2006).

96 well MAXISorp plates (NUNC) were coated over night with 2 ug/mlstreptavidin in PBS at room temperature, washed 4× and blocked for 1 hat 37° C. in 2% BSA containing blocking buffer. RefoldedHLA-A*02:01/MLA-001 monomers served as standards, covering the range of15-500 ng/ml. Peptide-MHC monomers of the UV-exchange reaction werediluted 100 fold in blocking buffer. Samples were incubated for 1 h at37° C., washed four times, incubated with 2 ug/ml HRP conjugated anti-62m for 1 h at 37° C., washed again and detected with TMB solution that isstopped with NH₂SO₄. Absorption was measured at 450 nm. Candidatepeptides that show a high exchange yield (preferably higher than 50%,most preferred higher than 75%) are generally preferred for a generationand production of antibodies or fragments thereof, and/or T cellreceptors or fragments thereof, as they show sufficient avidity to theMHC molecules and prevent dissociation of the MHC complexes.

TABLE 16A MHC class I binding scoresBinding of HLA-class I restricted peptides toHLA-A*24 was evaluated by peptide ex- change yield: ≥10% = +; ≥20% = ++;≥50 = +++; ≥75% = ++++ SEQ ID Sequence Peptide exchange 24 SYNDALLTF +++25 IYEPYLAMF +++ 26 RYADDTFTPAF +++ 27 GYLQGLVSF ++++ 28 YYAKEIHKF ++++29 RYGSPINTF +++ 30 SYSPAHARL +++ 31 AYTSPPSFF +++ 32 PYQLNASLFTF ++++33 QYGKDFLTL +++ 34 AFSPDSHYLLF +++ 35 IYTRVTYYL ++ 36 RYMWINQEL +++ 41RYLQKIEEF +++ 42 TYIGQGYII +++ 43 AYIKNGQLF +++ 44 VYNTVSEGTHF +++ 45RYFKTPRKF ++ 47 SYTPVLNQF ++++ 48 AWAPKPYHKF +++ 54 AYSEKVTEF +++ 55LYFEKGEYF ++++ 56 LFHPEDTGQVF ++ 58 GYIDKVRQL ++ 59 IYPDVTYAF +++

TABLE 16B MHC class I binding scoresBinding of HLA-class I restricted peptides toHLA-A*02 was evaluated by peptide ex- change yield: ≥10% = +; ≥20% = ++;≥50 = +++; ≥75% = ++++ SEQ ID Sequence Peptide exchange  1 VTAQIGIVAV++++  2 SMLGEEIQL ++++  3 HLLEDIAHV ++++  4 ALLTFVWKL ++++  5 KIFSRLIYI+++  6 ALLESRVNL ++++  7 TLLQVVGVVSV ++  9 GMLNEAEGKAIKL +++ 10TLWRGPVVV +++ 11 YLEEECPAT ++ 13 AMAPNHAVV +++ 14 KMDEASAQLL ++ 15KMDEASAQLLA +++ 16 KMDEASAQL +++ 20 SLLSHQVLL +++ 21 YLNDSLRHV ++ 22SLYDSIAFI ++++ 49 SLFHPEDTGQV +++ 52 ALGDLVQSV +++ 53 YLLKDKGEYTL +++

Example 6

Absolute Quantitation of Tumor Associated Peptides Presented on the CellSurface

The generation of binders, such as antibodies and/or TCRs, is alaborious process, which may be conducted only for a number of selectedtargets. In the case of tumor-associated and -specific peptides,selection criteria include but are not restricted to exclusiveness ofpresentation and the density of peptide presented on the cell surface.In addition to the isolation and relative quantitation of peptides asdescribed herein, the inventors did analyze absolute peptide copies percell as described. The quantitation of TUMAP copies per cell in solidtumor samples requires the absolute quantitation of the isolated TUMAP,the efficiency of TUMAP isolation, and the cell count of the tissuesample analyzed.

Peptide Quantitation by NanoLC-MS/MS

For an accurate quantitation of peptides by mass spectrometry, acalibration curve was generated for each peptide using the internalstandard method. The internal standard is a double-isotope-labelledvariant of each peptide, i.e. two isotope-labelled amino acids wereincluded in TUMAP synthesis. It differs from the tumor-associatedpeptide only in its mass but shows no difference in otherphysicochemical properties (Anderson et al., 2012). The internalstandard was spiked to each MS sample and all MS signals were normalizedto the MS signal of the internal standard to level out potentialtechnical variances between MS experiments.

The calibration curves were prepared in at least three differentmatrices, i.e. HLA peptide eluates from natural samples similar to theroutine MS samples, and each preparation was measured in duplicate MSruns. For evaluation, MS signals were normalized to the signal of theinternal standard and a calibration curve was calculated by logisticregression.

For the quantitation of tumor-associated peptides from tissue samples,the respective samples were also spiked with the internal standard; theMS signals were normalized to the internal standard and quantified usingthe peptide calibration curve.

Efficiency of Peptide/MHC Isolation

As for any protein purification process, the isolation of proteins fromtissue samples is associated with a certain loss of the protein ofinterest. To determine the efficiency of TUMAP isolation, peptide/MHCcomplexes were generated for all TUMAPs selected for absolutequantitation. To be able to discriminate the spiked from the naturalpeptide/MHC complexes, single-isotope-labelled versions of the TUMAPswere used, i.e. one isotope-labelled amino acid was included in TUMAPsynthesis. These complexes were spiked into the freshly prepared tissuelysates, i.e. at the earliest possible point of the TUMAP isolationprocedure, and then captured like the natural peptide/MHC complexes inthe following affinity purification. Measuring the recovery of thesingle-labelled TUMAPs therefore allows conclusions regarding theefficiency of isolation of individual natural TUMAPs.

The efficiency of isolation was analyzed in a low number of samples andwas comparable among these tissue samples. In contrast, the isolationefficiency differs between individual peptides. This suggests that theisolation efficiency, although determined in only a limited number oftissue samples, may be extrapolated to any other tissue preparation.However, it is necessary to analyze each TU MAP individually as theisolation efficiency may not be extrapolated from one peptide to others.

Determination of the Cell Count in Solid, Frozen Tissue

In order to determine the cell count of the tissue samples subjected toabsolute peptide quantitation, the inventors applied DNA contentanalysis. This method is applicable to a wide range of samples ofdifferent origin and, most importantly, frozen samples (Alcoser et al.,2011; Forsey and Chaudhuri, 2009; Silva et al., 2013). During thepeptide isolation protocol, a tissue sample is processed to a homogenouslysate, from which a small lysate aliquot is taken. The aliquot isdivided in three parts, from which DNA is isolated (QiaAmp DNA Mini Kit,Qiagen, Hilden, Germany). The total DNA content from each DNA isolationis quantified using a fluorescence-based DNA quantitation assay (QubitdsDNA HS Assay Kit, Life Technologies, Darmstadt, Germany) in at leasttwo replicates.

In order to calculate the cell number, a DNA standard curve fromaliquots of single healthy blood cells, with a range of defined cellnumbers, has been generated. The standard curve is used to calculate thetotal cell content from the total DNA content from each DNA isolation.The mean total cell count of the tissue sample used for peptideisolation is extrapolated considering the known volume of the lysatealiquots and the total lysate volume.

Peptide Copies Per Cell

With data of the aforementioned experiments, the inventors calculatedthe number of TUMAP copies per cell by dividing the total peptide amountby the total cell count of the sample, followed by division throughisolation efficiency. Copy cell number for selected peptides are shownin Table 17.

TABLE 17 Absolute copy numbers. The table lists the results of absolutepeptide quantitation in tumor samples. SEQ ID Copies per cell No.Peptide Code (median) Number of samples 1 OR51E2-001 + 13 2 GREB-001 ++14 3 NEFH-001 ++ 11 4 TRPM8-002 +++ 6 5 TRPM8-003 ++ 6 6 PDE11-001 + 1024 TRPM8-004 +++ 15 26 RAB3B-001 ++ 15 27 KLK4-001 ++++ 16 28 TGFB3-001+++ 16 42 FKBP10-002 ++ 19 49 KLK3-004 + 15 50 LRRC26-001 ++ 13 54KLK2-001 +++ 16 55 ACPP-002 +++ 15 56 KLK3-005 +++ 16 57 FOLH1-005 +++16 The median number of copies per cell are indicated for each peptide:<100 = +; >=100 = ++; >=1,000 +++; >=10,000 = ++++. The number ofsamples, in which evaluable, high quality MS data are available isindicated.

REFERENCE LIST

-   Adachi, H. et al., Oncogene 23 (2004): 3495-3500-   Allison, J. P. et al., Science 270 (1995): 932-933-   American Cancer Society, (2015)-   Ammendola, M. et al., Biomed. Res. Int. 2014 (2014): 154702-   Andersen, R. S. et al., Nat. Protoc. 7 (2012): 891-902-   Andres, S. A. et al., BMC. Cancer 13 (2013): 326-   Appay, V. et al., Eur. J Immunol. 36 (2006): 1805-1814-   Arentz, G. et al., Clin Proteomics. 8 (2011): 16-   Banchereau, J. et al., Cell 106 (2001): 271-274-   Bausch, D. et al., Clin Cancer Res. 17 (2011): 302-309-   Beatty, G. et al., J Immunol 166 (2001): 2276-2282-   Beggs, J. D., Nature 275 (1978): 104-109-   Benjamini, Y. et al., Journal of the Royal Statistical Society.    Series B (Methodological), Vol. 57 (1995): 289-300-   Bhosle, R. C. et al., Biochem. Biophys. Res. Commun. 346 (2006):    768-777-   Bouameur, J. E. et al., J Invest Dermatol. 134 (2014): 885-894-   Boulter, J. M. et al., Protein Eng 16 (2003): 707-711-   Braumuller, H. et al., Nature (2013)-   Bresnick, E. H. et al., Nucleic Acids Res. 40 (2012): 5819-5831-   Brossart, P. et al., Blood 90 (1997): 1594-1599-   Bruckdorfer, T. et al., Curr. Pharm. Biotechnol. 5 (2004): 29-43-   Card, K. F. et al., Cancer Immunol. Immunother. 53 (2004): 345-357-   Chanock, S. J. et al., Hum. Immunol. 65 (2004): 1211-1223-   Chen, L. et al., Med. Oncol 30 (2013): 498-   Chong, I. W. et al., Oncol Rep. 16 (2006): 981-988-   Clemen, C. S. et al., Acta Neuropathol. 129 (2015): 297-315-   Cohen, C. J. et al., J Mol. Recognit. 16 (2003a): 324-332-   Cohen, C. J. et al., J Immunol. 170 (2003b): 4349-4361-   Cohen, S. N. et al., Proc. Natl. Acad. Sci. U.S.A 69 (1972):    2110-2114-   Coligan, J. E. et al., Current Protocols in Protein Science (1995)-   Colombetti, S. et al., J Immunol. 176 (2006): 2730-2738-   Davidson, B. et al., Hum. Pathol. 45 (2014): 691-700-   Deng, M. et al., Oncogene 32 (2013): 4273-4283-   Dengjel, J. et al., Clin Cancer Res 12 (2006): 4163-4170-   Denkberg, G. et al., J Immunol. 171 (2003): 2197-2207-   Dubrowinskaja, N. et al., Cancer Med. (2014)-   Falk, K. et al., Nature 351 (1991): 290-296-   Faucz, F. R. et al., J Clin Endocrinol. Metab 96 (2011): E135-E140-   Fawcett, L. et al., Proc. Natl. Acad. Sci. U.S.A 97 (2000):    3702-3707-   Fong, L. et al., Proc. Natl. Acad. Sci. U.S.A 98 (2001): 8809-8814-   Forti, S. et al., Breast Cancer Res Treat. 73 (2002): 245-256-   Frattini, V. et al., Nat Genet. 45 (2013): 1141-1149-   Fu, C. A. et al., J Biol. Chem. 274 (1999): 30729-30737-   Gabrilovich, D. I. et al., Nat. Med 2 (1996): 1096-1103-   Gattinoni, L. et al., Nat. Rev. Immunol. 6 (2006): 383-393-   Gnjatic, S. et al., Proc Natl. Acad. Sci. U.S.A 100 (2003):    8862-8867-   Godkin, A. et al., Int. Immunol 9 (1997): 905-911-   Graddis, T. J. et al., Int. J Clin Exp. Pathol. 4 (2011): 295-306-   Green, M. R. et al., Molecular Cloning, A Laboratory Manual 4th    (2012)-   Greene, M. H. et al., Endocr. Relat Cancer 17 (2010): R109-R121-   Greenfield, E. A., Antibodies: A Laboratory Manual 2nd (2014)-   Grunewald, T. G. et al., Biol. Cell 104 (2012): 641-657-   Gutman, G. A. et al., Pharmacol. Rev. 57 (2005): 473-508-   Haferlach, C. et al., Haematologica 96 (2011): 829-836-   Hale, L. P. et al., Clinical Cancer Research 7 (2001): 846-853-   Hallen, A. et al., J Neurochem. 118 (2011): 379-387-   Halpain, S. et al., Genome Biol. 7 (2006): 224-   Hanahan, D. et al., Cell 100 (2000): 57-70-   Hassan, M. I. et al., Mol Cancer Res 6 (2008): 892-906-   Higgins, G. et al., Proc. Natl. Acad. Sci. U.S.A 109 (2012):    E3128-E3135-   Ho, L. L. et al., Prostate 68 (2008): 1421-1429-   Horvath, A. et al., Curr. Opin. Endocrinol. Diabetes Obes. 15    (2008): 227-233-   Hu, J. C. et al., Gene 251 (2000): 1-8-   Hwang, M. L. et al., J Immunol. 179 (2007): 5829-5838-   Hyodo, T. et al., J Biol. Chem. 287 (2012): 25019-25029-   Ito, S. et al., Head Neck 32 (2010a): 96-103-   Ito, Y. et al., Proc. Natl. Acad. Sci. U.S.A 107 (2010b):    10538-10542-   Jiao, X. et al., BMC. Genomics 14 (2013): 165-   Jin, Y. et al., Proc. Natl. Acad. Sci. U.S.A 110 (2013): E2572-E2581-   Jung, G. et al., Proc Natl Acad Sci USA 84 (1987): 4611-4615-   Kai, F. et al., Oncotarget. 6 (2015): 11162-11174-   Kandimalla, R. et al., Eur. Urol. 61 (2012): 1245-1256-   Katada, K. et al., J Proteomics. 75 (2012): 1803-1815-   Katoh, Y. et al., Cancer Biol. Ther. 4 (2005): 1050-1054-   Kibbe, A. H., Handbook of Pharmaceutical Excipients rd (2000)-   Kibel, A. S. et al., Int. J Cancer 109 (2004): 668-672-   Kinameri, E. et al., PLoS. ONE. 3 (2008): e3859-   Klejnot, M. et al., Acta Crystallogr. D. Biol. Crystallogr. 68    (2012): 154-159-   Krieg, A. M., Nat. Rev. Drug Discov. 5 (2006): 471-484-   Lapointe, J. et al., Proc. Natl. Acad. Sci. U.S.A 101 (2004):    811-816-   Laviolette, L. A. et al., Int. J Cancer 135 (2014): 1072-1084-   Lee, K. Y. et al., J Med. 35 (2004): 141-149-   Li, Y. W. et al., PLoS. ONE. 9 (2014): e87505-   Li, Z. J. et al., Development 139 (2012): 4152-4161-   Liddy, N. et al., Nat. Med. 18 (2012): 980-987-   Liu, P. et al., Science 261 (1993): 1041-1044-   Liu, Y. H. et al., Biochem. Biophys. Res Commun. 404 (2011): 488-493-   Ljunggren, H. G. et al., J Exp. Med 162 (1985): 1745-1759-   Longenecker, B. M. et al., Ann N.Y. Acad. Sci. 690 (1993): 276-291-   Lue, H. W. et al., PLoS. ONE. 6 (2011): e27720-   Lukas, T. J. et al., Proc. Natl. Acad. Sci. U.S.A 78 (1981):    2791-2795-   Lundblad, R. L., Chemical Reagents for Protein Modification 3rd    (2004)-   Ma, Y. et al., Mol Cell Proteomics. 8 (2009): 1878-1890-   Malinowska, K. et al., Prostate 69 (2009): 1109-1118-   Matsumoto, F. et al., Hum. Pathol. 37 (2006): 1592-1600-   Matsuoka, R. et al., Am. J Med. Genet. 46 (1993): 61-67-   Meziere, C. et al., J Immunol 159 (1997): 3230-3237-   Midorikawa, Y. et al., Jpn. J Cancer Res. 93 (2002): 636-643-   Montani, M. et al., Virchows Arch. 462 (2013): 437-443-   Morgan, R. A. et al., Science 314 (2006): 126-129-   Mori, M. et al., Transplantation 64 (1997): 1017-1027-   Mortara, L. et al., Clin Cancer Res. 12 (2006): 3435-3443-   Mueller, L. N. et al., J Proteome. Res. 7 (2008): 51-61-   Mueller, L. N. et al., Proteomics. 7 (2007): 3470-3480-   Mumberg, D. et al., Proc. Natl. Acad. Sci. U.S.A 96 (1999):    8633-8638-   Nicke, B. et al., Mol. Cell 20 (2005): 673-685-   Nishibe, R. et al., FEBS Lett. 587 (2013): 1529-1535-   Nishidate, T. et al., Int. J Oncol 25 (2004): 797-819-   Noetzel, E. et al., Oncogene 29 (2010): 4814-4825-   Olesen, S. H. et al., Mol Cell Proteomics. 4 (2005): 534-544-   Peters, I. et al., Target Oncol (2014)-   Petrella, B. L. et al., Cancer Lett. 325 (2012): 220-226-   Pinheiro, J. et al., nlme: Linear and Nonlinear Mixed Effects Models    (2015)-   Plebanski, M. et al., Eur. J Immunol 25 (1995): 1783-1787-   Porta, C. et al., Virology 202 (1994): 949-955-   Prevarskaya, N. et al., Biochim. Biophys. Acta 1772 (2007): 937-946-   Quinn, D. I. et al., Urol. Oncol 33 (2015): 245-260-   Quinn, M. C. et al., Int. J Oncol 42 (2013): 912-920-   Rae, J. M. et al., Prostate 66 (2006): 886-894-   Rammensee, H. G. et al., Immunogenetics 50 (1999): 213-219-   RefSeq, The NCBI handbook [Internet], Chapter 18, (2002).-   Rini, B. I. et al., Cancer 107 (2006): 67-74-   Rizzardi, A. E. et al., BMC. Cancer 14 (2014): 244-   Rock, K. L. et al., Science 249 (1990): 918-921-   Rotondo, F. et al., Appl. Immunohistochem. Mol. Morphol. 17 (2009):    185-188-   Russel, F. G. et al., Trends Pharmacol. Sci. 29 (2008): 200-207-   S3-Leitlinie Prostatakarzinom, 043/022OL, (2014)-   Saiki, R. K. et al., Science 239 (1988): 487-491-   Sakai, T. et al., J Pharmacol. Sci. 98 (2005): 41-48-   Schmitt, M. et al., Radiol. Oncol. 47 (2013): 319-329-   Seeger, F. H. et al., Immunogenetics 49 (1999): 571-576-   SEER Stat facts, (2014)-   Severi, G. et al., Cancer Med. 3 (2014): 1266-1274-   Shaheduzzaman, S. et al., Cancer Biol. Ther 6 (2007): 1088-1095-   Sherman, F. et al., Laboratory Course Manual for Methods in Yeast    Genetics (1986)-   Shkoda, A. et al., PLoS. Biol. 10 (2012): e1001376-   Singh-Jasuja, H. et al., Cancer Immunol. Immunother. 53 (2004):    187-195-   Small, E. J. et al., J Clin Oncol. 24 (2006): 3089-3094-   Sturm, M. et al., BMC. Bioinformatics. 9 (2008): 163-   Sudhof, T. C., Neuron 75 (2012): 11-25-   Sun, Z. et al., J Proteome. Res 13 (2014): 1593-1601-   Tan, L. Z. et al., Am. J Pathol. 183 (2013): 831-840-   Tan, P. Y. et al., Mol. Cell Biol. 32 (2012): 399-414-   Teufel, R. et al., Cell Mol. Life Sci. 62 (2005): 1755-1762-   Tran, E. et al., Science 344 (2014): 641-645-   Tsavaler, L. et al., Cancer Research 61 (2001): 3760-3769-   UniProt, (2015)-   Walter, S. et al., J. Immunol. 171 (2003): 4974-4978-   Walter, S. et al., Nat Med. 18 (2012): 1254-1261-   Wang, J. et al., Arch. Pharm. Res 34 (2011): 987-995-   Wang, L. et al., Cancer Research 70 (2010): 5818-5828-   Wang, R. J. et al., Asian Pac. J Cancer Prev. 15 (2014): 7223-7228-   Wang, Y. et al., Hum. Mol. Genet. 21 (2012): 569-576-   Wang, Z. et al., Med. Oncol 32 (2015): 87-   Ward, P. P. et al., Cell Mol Life Sci. 62 (2005): 2540-2548-   Weng, J. et al., Int. J Cancer 113 (2005): 811-818-   Westdorp, H. et al., Front Immunol. 5 (2014): 191-   Whiteland, H. et al., Clin Exp. Metastasis 31 (2014): 909-920-   Willcox, B. E. et al., Protein Sci. 8 (1999): 2418-2423-   Willoughby, V. et al., Appl. Immunohistochem. Mol. Morphol. 16    (2008): 344-348-   Wilson, P. M. et al., J Neurosci. 30 (2010): 8529-8540-   World Cancer Report, (2014)-   Wu, J. P. et al., Asian J Androl 16 (2014): 710-714-   Yamamoto, G. L. et al., J Med. Genet. 52 (2015): 413-421-   Yang, Z. et al., J Virol. 81 (2007): 6294-6306-   Ye, Q. et al., PLoS. ONE. 9 (2014): e103298-   Yin, J. et al., Mol. Med. Rep. 8 (2013): 1630-1634-   Yu, Y. P. et al., Urology 68 (2006): 578-582-   Zaremba, S. et al., Cancer Res. 57 (1997): 4570-4577-   Zhang, G. et al., Oncol Rep. (2014)-   Zhao, X. et al., Onco. Targets. Ther 7 (2014): 343-351

The invention claimed is:
 1. A method of eliciting an immune response ina patient who has prostate cancer, comprising administering to saidpatient a composition comprising a population of activated T cells thatselectively recognize cells in the patient that aberrantly express apeptide, wherein said peptide consisting of the amino acid sequence ofAYSEKVTEF (SEQ ID NO: 54), wherein the activated T cells are cytotoxic Tcells produced by contacting T cells with an antigen presenting cellthat expresses the peptide in a complex with an MHC class I molecule onthe surface of the antigen presenting cell, for a period of timesufficient to activate said T cell specifically against the peptide, andwherein the antigen presenting cell is a particle coated with thepeptide in a complex with an MHC class I molecule.
 2. The method ofclaim 1, wherein the T cells are autologous to the patient.
 3. Themethod of claim 1, wherein the T cells are obtained from a healthydonor.
 4. The method of claim 1, wherein the T cells are obtained fromtumor infiltrating lymphocytes or peripheral blood mononuclear cells. 5.The method of claim 1, further comprising expanding T cells in vitro. 6.The method of claim 1, wherein the MHC molecule is a class I molecule.7. The method of claim 1, wherein the composition further comprises anadjuvant.
 8. The method of claim 7, wherein the adjuvant is selectedfrom the group consisting of imiquimod, resiguimod, GM-CSF,cyclophosphamide, Sunitinib, bevacizumab, interferon-alpha, CpG,oligonucleotides and derivatives, poly-(I:C) and derivatives, RNA,sildenafil, and particulate formations with PLG and virosomes.
 9. Themethod of claim 1, further comprising stimulating the activated T cellsin the presence of an anti-CD28 antibody and IL-12 to clonally expandthe T cells.
 10. The method of claim 1, wherein the population ofactivated T cells comprises CD8-positive cells.
 11. The method of claim1, wherein the contacting is in vitro.
 12. The method of claim 1,wherein the particle is further coated with an anti-CD28 antibody. 13.The method of claim 1, wherein the particle is polystyrene particle.